Starting phenix.real_space_refine on Tue Aug 26 04:37:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8w_36966/08_2025/8k8w_36966.cif" } resolution = 3.46 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= 0.004 sd= 0.025 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 42 5.16 5 C 21150 2.51 5 N 6000 2.21 5 O 6264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33456 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Time building chain proxies: 7.35, per 1000 atoms: 0.22 Number of scatterers: 33456 At special positions: 0 Unit cell: (150.88, 166.46, 175.48, 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 42 16.00 O 6264 8.00 N 6000 7.00 C 21150 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: 3.19 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 58 sheets defined 53.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.663A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 119 removed outlier: 4.269A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 152 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.230A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 241 removed outlier: 3.662A pdb=" N ARG D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 293 through 297 removed outlier: 3.536A pdb=" N ILE D 297 " --> pdb=" O VAL D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 321 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 363 through 372 removed outlier: 4.074A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.847A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.790A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 removed outlier: 3.808A pdb=" N TYR D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 3.818A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 removed outlier: 3.952A pdb=" N GLU D 716 " --> pdb=" O GLY D 712 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP D 717 " --> pdb=" O HIS D 713 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 719 " --> pdb=" O LYS D 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 96 through 120 removed outlier: 4.435A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 removed outlier: 3.769A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.040A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.646A pdb=" N GLN C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.645A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.859A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.790A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 543 through 557 removed outlier: 3.574A pdb=" N TYR C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 653 removed outlier: 3.735A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 718 removed outlier: 3.899A pdb=" N GLU C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 717 " --> pdb=" O HIS C 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.503A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 119 removed outlier: 4.057A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 152 removed outlier: 3.646A pdb=" N GLU B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.382A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.747A pdb=" N ILE B 297 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.806A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 4.053A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.904A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 636 removed outlier: 3.715A pdb=" N LYS B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 removed outlier: 3.846A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 removed outlier: 3.517A pdb=" N GLU B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 717 " --> pdb=" O HIS B 713 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 719 " --> pdb=" O LYS B 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.656A pdb=" N GLU A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.219A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 241 removed outlier: 3.525A pdb=" N ALA A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.143A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.624A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.763A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.602A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.044A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.557A pdb=" N ALA A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 717 removed outlier: 3.522A pdb=" N GLU A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 717 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 9 removed outlier: 3.532A pdb=" N LEU F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.571A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 120 removed outlier: 4.481A pdb=" N HIS F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 151 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.422A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 293 through 297 removed outlier: 3.670A pdb=" N ILE F 297 " --> pdb=" O VAL F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.696A pdb=" N GLN F 306 " --> pdb=" O HIS F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 363 through 372 removed outlier: 3.700A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 380 removed outlier: 4.181A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 413 through 428 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 543 through 557 removed outlier: 4.144A pdb=" N TYR F 557 " --> pdb=" O LEU F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 removed outlier: 3.515A pdb=" N LEU F 588 " --> pdb=" O GLY F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 654 removed outlier: 4.559A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 654 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 removed outlier: 3.740A pdb=" N ALA F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 717 removed outlier: 3.707A pdb=" N ASP F 717 " --> pdb=" O HIS F 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.695A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 119 removed outlier: 4.054A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 151 Processing helix chain 'E' and resid 173 through 221 removed outlier: 3.930A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.522A pdb=" N GLN E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.523A pdb=" N ILE E 297 " --> pdb=" O VAL E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.617A pdb=" N GLU E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.818A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 451 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.715A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.753A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.162A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 716 removed outlier: 4.015A pdb=" N GLU E 716 " --> pdb=" O GLY E 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.520A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AA3, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AA5, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AA6, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.484A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AA8, first strand: chain 'D' and resid 498 through 505 removed outlier: 3.765A pdb=" N TRP D 511 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS D 527 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 604 through 606 removed outlier: 6.332A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 609 through 610 removed outlier: 3.532A pdb=" N ALA D 609 " --> pdb=" O LEU D 617 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.663A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS C 48 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG C 383 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR C 50 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU C 385 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 52 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 253 through 254 removed outlier: 7.411A pdb=" N VAL C 88 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB6, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AB8, first strand: chain 'C' and resid 528 through 530 removed outlier: 6.842A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.229A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 609 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.528A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 253 through 256 removed outlier: 6.660A pdb=" N LEU B 78 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 88 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AC6, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.487A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AC8, first strand: chain 'B' and resid 498 through 505 removed outlier: 3.784A pdb=" N TRP B 511 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 604 through 606 removed outlier: 6.547A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.684A pdb=" N ALA B 609 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.664A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 52 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AD4, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AD5, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AD6, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AD7, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AD8, first strand: chain 'A' and resid 410 through 411 removed outlier: 6.894A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AE1, first strand: chain 'A' and resid 528 through 530 removed outlier: 6.776A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP A 511 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AE3, first strand: chain 'F' and resid 20 through 21 removed outlier: 4.669A pdb=" N LEU F 411 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.562A pdb=" N VAL F 267 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA F 49 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY F 362 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU F 51 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR F 50 " --> pdb=" O ALA F 384 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 253 through 254 removed outlier: 4.518A pdb=" N VAL F 90 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 156 through 158 Processing sheet with id=AE7, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AE8, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AE9, first strand: chain 'F' and resid 494 through 495 Processing sheet with id=AF1, first strand: chain 'F' and resid 498 through 505 removed outlier: 4.067A pdb=" N TRP F 511 " --> pdb=" O VAL F 505 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG F 516 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 604 through 606 removed outlier: 6.254A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 609 through 610 removed outlier: 3.516A pdb=" N ALA F 609 " --> pdb=" O LEU F 617 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.634A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AF6, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AF7, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF8, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF9, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.267A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AG2, first strand: chain 'E' and resid 498 through 505 removed outlier: 3.998A pdb=" N TRP E 511 " --> pdb=" O VAL E 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 516 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 583 through 584 removed outlier: 3.935A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.655A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 1830 hydrogen bonds defined for protein. 5292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.17 Time building geometry restraints manager: 4.14 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: 11632 1.34 - 1.46: 5121 1.46 - 1.57: 17296 1.57 - 1.69: 1 1.69 - 1.81: 72 Bond restraints: 34122 Sorted by residual: bond pdb=" CA THR A 159 " pdb=" CB THR A 159 " ideal model delta sigma weight residual 1.525 1.577 -0.053 1.47e-02 4.63e+03 1.28e+01 bond pdb=" CA THR D 159 " pdb=" CB THR D 159 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.33e-02 5.65e+03 2.83e+00 bond pdb=" CA THR E 159 " pdb=" CB THR E 159 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CB TYR B 575 " pdb=" CG TYR B 575 " ideal model delta sigma weight residual 1.512 1.544 -0.032 2.20e-02 2.07e+03 2.09e+00 bond pdb=" C ALA A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.99e+00 ... (remaining 34117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 44753 1.36 - 2.73: 1302 2.73 - 4.09: 216 4.09 - 5.45: 43 5.45 - 6.82: 12 Bond angle restraints: 46326 Sorted by residual: angle pdb=" C GLU F 579 " pdb=" CA GLU F 579 " pdb=" CB GLU F 579 " ideal model delta sigma weight residual 116.54 110.15 6.39 1.15e+00 7.56e-01 3.08e+01 angle pdb=" CA GLU F 579 " pdb=" C GLU F 579 " pdb=" N GLY F 580 " ideal model delta sigma weight residual 119.52 116.39 3.13 7.90e-01 1.60e+00 1.57e+01 angle pdb=" C PHE E 386 " pdb=" N SER E 387 " pdb=" CA SER E 387 " ideal model delta sigma weight residual 121.20 116.06 5.14 1.40e+00 5.10e-01 1.35e+01 angle pdb=" C ALA E 507 " pdb=" N ALA E 508 " pdb=" CA ALA E 508 " ideal model delta sigma weight residual 122.06 127.20 -5.14 1.45e+00 4.76e-01 1.26e+01 angle pdb=" N ILE E 558 " pdb=" CA ILE E 558 " pdb=" C ILE E 558 " ideal model delta sigma weight residual 111.77 108.18 3.59 1.04e+00 9.25e-01 1.19e+01 ... (remaining 46321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 18982 18.02 - 36.03: 1155 36.03 - 54.05: 251 54.05 - 72.07: 187 72.07 - 90.08: 149 Dihedral angle restraints: 20724 sinusoidal: 8394 harmonic: 12330 Sorted by residual: dihedral pdb=" CA ASN B 574 " pdb=" C ASN B 574 " pdb=" N TYR B 575 " pdb=" CA TYR B 575 " ideal model delta harmonic sigma weight residual 180.00 -135.27 -44.73 0 5.00e+00 4.00e-02 8.00e+01 dihedral pdb=" CA ASN F 574 " pdb=" C ASN F 574 " pdb=" N TYR F 575 " pdb=" CA TYR F 575 " ideal model delta harmonic sigma weight residual -180.00 -139.74 -40.26 0 5.00e+00 4.00e-02 6.48e+01 dihedral pdb=" CA ASN D 574 " pdb=" C ASN D 574 " pdb=" N TYR D 575 " pdb=" CA TYR D 575 " ideal model delta harmonic sigma weight residual -180.00 -142.89 -37.11 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3460 0.030 - 0.061: 1212 0.061 - 0.091: 336 0.091 - 0.122: 139 0.122 - 0.152: 19 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CA ARG D 287 " pdb=" N ARG D 287 " pdb=" C ARG D 287 " pdb=" CB ARG D 287 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE F 359 " pdb=" N ILE F 359 " pdb=" C ILE F 359 " pdb=" CB ILE F 359 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR E 159 " pdb=" CA THR E 159 " pdb=" OG1 THR E 159 " pdb=" CG2 THR E 159 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 574 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ASN F 574 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN F 574 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR F 575 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 574 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ASN D 574 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN D 574 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR D 575 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 574 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASN B 574 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN B 574 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR B 575 " 0.020 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 616 2.70 - 3.25: 34074 3.25 - 3.80: 55890 3.80 - 4.35: 70899 4.35 - 4.90: 117928 Nonbonded interactions: 279407 Sorted by model distance: nonbonded pdb=" OE1 GLU E 111 " pdb=" OH TYR E 209 " model vdw 2.154 3.040 nonbonded pdb=" NH2 ARG B 516 " pdb=" OE2 GLU B 572 " model vdw 2.155 3.120 nonbonded pdb=" OE2 GLU A 579 " pdb=" OG SER A 582 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU A 40 " pdb=" OH TYR A 66 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG E 319 " pdb=" OE2 GLU E 320 " model vdw 2.253 3.120 ... (remaining 279402 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.670 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.002 0.053 34122 Z= 0.132 Angle : 0.566 6.815 46326 Z= 0.330 Chirality : 0.036 0.152 5166 Planarity : 0.004 0.058 6186 Dihedral : 16.463 90.082 12804 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 1.10 (0.13), residues: 4302 helix: 1.93 (0.11), residues: 2205 sheet: -0.99 (0.22), residues: 512 loop : -0.33 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 328 TYR 0.014 0.001 TYR E 271 PHE 0.016 0.001 PHE C 571 TRP 0.014 0.001 TRP F 10 HIS 0.007 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00239 (34122) covalent geometry : angle 0.56623 (46326) hydrogen bonds : bond 0.14304 ( 1830) hydrogen bonds : angle 5.25907 ( 5292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 LEU cc_start: 0.8506 (tp) cc_final: 0.8301 (pp) REVERT: D 124 PHE cc_start: 0.6713 (t80) cc_final: 0.5989 (t80) REVERT: D 334 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8418 (pp30) REVERT: D 342 GLN cc_start: 0.8654 (mt0) cc_final: 0.8201 (mp10) REVERT: D 498 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7604 (mt-10) REVERT: D 688 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7606 (tpt-90) REVERT: C 40 GLU cc_start: 0.7730 (tt0) cc_final: 0.7498 (tt0) REVERT: C 124 PHE cc_start: 0.5907 (t80) cc_final: 0.5178 (t80) REVERT: C 128 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8831 (pttp) REVERT: C 132 GLU cc_start: 0.8091 (tt0) cc_final: 0.7836 (tm-30) REVERT: C 289 VAL cc_start: 0.7674 (t) cc_final: 0.6988 (t) REVERT: C 334 GLN cc_start: 0.8029 (pp30) cc_final: 0.7817 (pt0) REVERT: C 510 TYR cc_start: 0.8208 (p90) cc_final: 0.7694 (p90) REVERT: C 689 MET cc_start: 0.5683 (mmt) cc_final: 0.5478 (mmm) REVERT: B 74 THR cc_start: 0.8116 (p) cc_final: 0.7839 (p) REVERT: B 254 LEU cc_start: 0.8218 (mt) cc_final: 0.7780 (pp) REVERT: B 267 VAL cc_start: 0.9401 (t) cc_final: 0.9059 (p) REVERT: B 313 ASP cc_start: 0.8041 (m-30) cc_final: 0.7541 (t0) REVERT: B 363 THR cc_start: 0.7761 (p) cc_final: 0.7561 (p) REVERT: B 373 ASP cc_start: 0.8198 (m-30) cc_final: 0.7317 (m-30) REVERT: B 378 GLU cc_start: 0.8308 (tt0) cc_final: 0.7989 (tm-30) REVERT: B 476 GLU cc_start: 0.8415 (tt0) cc_final: 0.8128 (mt-10) REVERT: B 554 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7789 (mtm-85) REVERT: B 662 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7645 (tp30) REVERT: A 356 MET cc_start: 0.3418 (pmm) cc_final: 0.3051 (ptp) REVERT: A 689 MET cc_start: 0.2172 (mtt) cc_final: 0.1900 (mtt) REVERT: F 15 GLU cc_start: 0.3029 (mm-30) cc_final: 0.2337 (mt-10) REVERT: F 103 GLU cc_start: 0.7905 (mp0) cc_final: 0.7685 (pp20) REVERT: F 140 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5810 (tm-30) REVERT: F 250 TRP cc_start: 0.5939 (m100) cc_final: 0.5578 (m100) REVERT: F 282 ASP cc_start: 0.5130 (m-30) cc_final: 0.4756 (t0) REVERT: F 433 MET cc_start: 0.4602 (ppp) cc_final: 0.4238 (ptm) REVERT: F 547 LEU cc_start: 0.7887 (tp) cc_final: 0.7596 (mt) REVERT: F 632 VAL cc_start: 0.2362 (t) cc_final: 0.2025 (m) REVERT: F 708 ARG cc_start: 0.5834 (mmp80) cc_final: 0.5273 (tmt170) REVERT: F 714 ASP cc_start: 0.3709 (m-30) cc_final: 0.3443 (t0) REVERT: F 717 ASP cc_start: 0.4337 (t0) cc_final: 0.4090 (t0) REVERT: E 26 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.7211 (Cg_exo) REVERT: E 269 GLU cc_start: 0.6926 (tp30) cc_final: 0.6650 (tp30) REVERT: E 320 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7734 (tt0) REVERT: E 431 ASP cc_start: 0.7946 (m-30) cc_final: 0.7680 (t0) REVERT: E 644 VAL cc_start: 0.7665 (p) cc_final: 0.7460 (t) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.2478 time to fit residues: 181.1255 Evaluate side-chains 211 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 334 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 141 GLN B 483 GLN B 597 ASN B 612 GLN A 97 GLN A 253 ASN A 334 GLN F 60 HIS F 113 ASN F 303 HIS F 543 HIS F 650 ASN F 653 ASN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.148641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.100013 restraints weight = 77044.078| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.46 r_work: 0.3275 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 34122 Z= 0.275 Angle : 0.686 13.172 46326 Z= 0.340 Chirality : 0.043 0.260 5166 Planarity : 0.005 0.102 6186 Dihedral : 4.271 43.716 4803 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 1.35 % Allowed : 7.13 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.77 (0.13), residues: 4302 helix: 1.58 (0.11), residues: 2240 sheet: -1.06 (0.21), residues: 527 loop : -0.42 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 34 TYR 0.027 0.002 TYR B 575 PHE 0.030 0.002 PHE E 119 TRP 0.020 0.002 TRP E 205 HIS 0.009 0.002 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00634 (34122) covalent geometry : angle 0.68632 (46326) hydrogen bonds : bond 0.04257 ( 1830) hydrogen bonds : angle 4.59375 ( 5292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 PHE cc_start: 0.7112 (t80) cc_final: 0.5841 (t80) REVERT: D 287 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.7953 (mtp85) REVERT: D 498 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 688 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.7939 (tpt-90) REVERT: D 689 MET cc_start: 0.7129 (mmt) cc_final: 0.6840 (mmp) REVERT: C 124 PHE cc_start: 0.5861 (t80) cc_final: 0.5353 (t80) REVERT: C 125 LEU cc_start: 0.8655 (mt) cc_final: 0.8403 (mt) REVERT: C 128 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8850 (pttp) REVERT: C 132 GLU cc_start: 0.8160 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 405 LEU cc_start: 0.8602 (mt) cc_final: 0.8401 (mt) REVERT: A 689 MET cc_start: 0.2358 (mtt) cc_final: 0.1933 (mtt) REVERT: F 140 GLU cc_start: 0.6504 (mt-10) cc_final: 0.5654 (tm-30) REVERT: F 250 TRP cc_start: 0.6251 (m100) cc_final: 0.5842 (m100) REVERT: F 282 ASP cc_start: 0.4625 (m-30) cc_final: 0.4190 (t0) REVERT: F 433 MET cc_start: 0.5033 (ppp) cc_final: 0.4649 (ptm) REVERT: F 708 ARG cc_start: 0.5939 (mmp80) cc_final: 0.5189 (tmt170) REVERT: F 714 ASP cc_start: 0.2793 (m-30) cc_final: 0.2393 (t0) REVERT: E 320 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7881 (tp30) outliers start: 46 outliers final: 24 residues processed: 250 average time/residue: 0.2064 time to fit residues: 83.5089 Evaluate side-chains 180 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain E residue 205 TRP Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 346 optimal weight: 30.0000 chunk 233 optimal weight: 40.0000 chunk 363 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 612 GLN C 60 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 543 HIS E 212 ASN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.147052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097186 restraints weight = 75662.026| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.14 r_work: 0.3200 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34122 Z= 0.203 Angle : 0.593 13.825 46326 Z= 0.294 Chirality : 0.040 0.192 5166 Planarity : 0.005 0.069 6186 Dihedral : 4.090 42.855 4800 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 1.64 % Allowed : 8.98 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.76 (0.13), residues: 4302 helix: 1.57 (0.11), residues: 2223 sheet: -1.09 (0.22), residues: 513 loop : -0.39 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 225 TYR 0.022 0.002 TYR B 575 PHE 0.029 0.002 PHE E 119 TRP 0.013 0.001 TRP E 205 HIS 0.010 0.001 HIS B 560 Details of bonding type rmsd covalent geometry : bond 0.00464 (34122) covalent geometry : angle 0.59295 (46326) hydrogen bonds : bond 0.04035 ( 1830) hydrogen bonds : angle 4.40760 ( 5292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 PHE cc_start: 0.6898 (t80) cc_final: 0.5684 (t80) REVERT: D 287 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.7909 (mtp85) REVERT: D 498 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7665 (mt-10) REVERT: D 688 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.7882 (tpt90) REVERT: C 124 PHE cc_start: 0.5867 (t80) cc_final: 0.5274 (t80) REVERT: C 125 LEU cc_start: 0.8697 (mt) cc_final: 0.8489 (mt) REVERT: C 128 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8818 (pttp) REVERT: C 132 GLU cc_start: 0.8319 (tt0) cc_final: 0.8018 (tm-30) REVERT: B 86 ARG cc_start: 0.8038 (mpt180) cc_final: 0.7663 (mtt90) REVERT: B 646 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8764 (pp) REVERT: A 405 LEU cc_start: 0.8580 (mt) cc_final: 0.8234 (mt) REVERT: F 140 GLU cc_start: 0.6480 (mt-10) cc_final: 0.5682 (tm-30) REVERT: F 282 ASP cc_start: 0.5023 (m-30) cc_final: 0.4484 (t0) REVERT: F 433 MET cc_start: 0.5161 (ppp) cc_final: 0.4892 (ptm) REVERT: F 708 ARG cc_start: 0.5982 (mmp80) cc_final: 0.5251 (tmt170) REVERT: F 714 ASP cc_start: 0.2499 (m-30) cc_final: 0.2129 (t0) REVERT: E 155 PHE cc_start: 0.4251 (m-80) cc_final: 0.3990 (m-80) REVERT: E 320 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7980 (mm-30) outliers start: 56 outliers final: 31 residues processed: 214 average time/residue: 0.1848 time to fit residues: 65.7215 Evaluate side-chains 184 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 123 optimal weight: 0.0020 chunk 385 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 339 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 302 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 408 optimal weight: 6.9990 chunk 373 optimal weight: 30.0000 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN F 141 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.148752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099831 restraints weight = 75070.592| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.18 r_work: 0.3253 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34122 Z= 0.122 Angle : 0.532 12.273 46326 Z= 0.261 Chirality : 0.038 0.213 5166 Planarity : 0.004 0.047 6186 Dihedral : 3.910 41.059 4800 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.41 % Allowed : 10.15 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.93 (0.13), residues: 4302 helix: 1.70 (0.11), residues: 2226 sheet: -0.96 (0.22), residues: 513 loop : -0.32 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.020 0.002 TYR B 575 PHE 0.031 0.001 PHE E 119 TRP 0.018 0.001 TRP F 290 HIS 0.008 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00269 (34122) covalent geometry : angle 0.53188 (46326) hydrogen bonds : bond 0.03611 ( 1830) hydrogen bonds : angle 4.16051 ( 5292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7529 (ttp-170) REVERT: D 287 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.7954 (mmm160) REVERT: D 498 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7561 (mt-10) REVERT: D 688 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.7892 (tpt90) REVERT: C 124 PHE cc_start: 0.5859 (t80) cc_final: 0.5275 (t80) REVERT: C 128 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8797 (pttp) REVERT: C 132 GLU cc_start: 0.8362 (tt0) cc_final: 0.8044 (tm-30) REVERT: B 86 ARG cc_start: 0.8014 (mpt180) cc_final: 0.7644 (mtt90) REVERT: B 313 ASP cc_start: 0.8700 (m-30) cc_final: 0.8320 (m-30) REVERT: A 405 LEU cc_start: 0.8554 (mt) cc_final: 0.8185 (mt) REVERT: F 140 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5647 (tm-30) REVERT: F 282 ASP cc_start: 0.5150 (m-30) cc_final: 0.4564 (t0) REVERT: F 433 MET cc_start: 0.5395 (ppp) cc_final: 0.5029 (ptm) REVERT: F 708 ARG cc_start: 0.5758 (mmp80) cc_final: 0.5099 (tmt170) REVERT: F 714 ASP cc_start: 0.2398 (m-30) cc_final: 0.2019 (t0) REVERT: E 155 PHE cc_start: 0.4046 (m-80) cc_final: 0.3748 (m-80) REVERT: E 320 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8090 (mm-30) outliers start: 48 outliers final: 29 residues processed: 220 average time/residue: 0.1898 time to fit residues: 68.1820 Evaluate side-chains 194 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 228 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 412 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.145994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096110 restraints weight = 76832.919| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 4.48 r_work: 0.3185 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34122 Z= 0.202 Angle : 0.583 12.196 46326 Z= 0.288 Chirality : 0.040 0.188 5166 Planarity : 0.004 0.048 6186 Dihedral : 3.976 39.623 4800 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.72 % Rotamer: Outliers : 2.08 % Allowed : 10.65 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.84 (0.13), residues: 4302 helix: 1.60 (0.11), residues: 2231 sheet: -1.01 (0.22), residues: 524 loop : -0.30 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 34 TYR 0.023 0.002 TYR B 575 PHE 0.028 0.002 PHE E 119 TRP 0.012 0.001 TRP D 323 HIS 0.007 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00462 (34122) covalent geometry : angle 0.58348 (46326) hydrogen bonds : bond 0.03777 ( 1830) hydrogen bonds : angle 4.26482 ( 5292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7426 (ttp-170) REVERT: D 287 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.7951 (mmm160) REVERT: D 498 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 688 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.7961 (tpt90) REVERT: D 689 MET cc_start: 0.6992 (mmt) cc_final: 0.6734 (mmp) REVERT: C 124 PHE cc_start: 0.5891 (t80) cc_final: 0.5260 (t80) REVERT: C 128 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8747 (pttp) REVERT: C 132 GLU cc_start: 0.8366 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 207 LEU cc_start: 0.8529 (mt) cc_final: 0.8270 (pp) REVERT: B 40 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: B 646 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 651 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 405 LEU cc_start: 0.8481 (mt) cc_final: 0.8115 (mt) REVERT: F 140 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5649 (tm-30) REVERT: F 433 MET cc_start: 0.5414 (ppp) cc_final: 0.5157 (ptm) REVERT: F 708 ARG cc_start: 0.5706 (mmp80) cc_final: 0.5023 (tmt170) REVERT: F 714 ASP cc_start: 0.2531 (m-30) cc_final: 0.2108 (t0) REVERT: E 320 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8272 (mm-30) outliers start: 71 outliers final: 42 residues processed: 220 average time/residue: 0.1905 time to fit residues: 69.5636 Evaluate side-chains 198 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 367 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 410 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 378 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.148391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100292 restraints weight = 74580.324| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.71 r_work: 0.3269 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34122 Z= 0.114 Angle : 0.525 13.123 46326 Z= 0.256 Chirality : 0.038 0.210 5166 Planarity : 0.004 0.046 6186 Dihedral : 3.807 37.919 4800 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.28 % Rotamer: Outliers : 1.56 % Allowed : 11.85 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 1.01 (0.13), residues: 4302 helix: 1.72 (0.11), residues: 2233 sheet: -0.92 (0.22), residues: 526 loop : -0.20 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 688 TYR 0.023 0.002 TYR B 575 PHE 0.013 0.001 PHE E 155 TRP 0.011 0.001 TRP F 290 HIS 0.005 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00248 (34122) covalent geometry : angle 0.52462 (46326) hydrogen bonds : bond 0.03496 ( 1830) hydrogen bonds : angle 4.07701 ( 5292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7762 (ttm170) cc_final: 0.7491 (ttp-170) REVERT: D 287 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.7910 (mmm160) REVERT: D 498 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7532 (mt-10) REVERT: D 688 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.7967 (tpt90) REVERT: C 57 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8724 (tt) REVERT: C 124 PHE cc_start: 0.5842 (t80) cc_final: 0.5138 (t80) REVERT: C 128 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8757 (pttp) REVERT: C 207 LEU cc_start: 0.8525 (mt) cc_final: 0.8285 (pp) REVERT: B 313 ASP cc_start: 0.8694 (m-30) cc_final: 0.8306 (m-30) REVERT: B 646 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 651 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 385 GLU cc_start: 0.4793 (tt0) cc_final: 0.4385 (pt0) REVERT: A 405 LEU cc_start: 0.8516 (mt) cc_final: 0.8147 (mt) REVERT: F 140 GLU cc_start: 0.6459 (mt-10) cc_final: 0.5615 (tm-30) REVERT: F 282 ASP cc_start: 0.5384 (m-30) cc_final: 0.4616 (t0) REVERT: F 433 MET cc_start: 0.5490 (ppp) cc_final: 0.5118 (ptm) REVERT: F 708 ARG cc_start: 0.5751 (mmp80) cc_final: 0.5078 (tmt170) REVERT: F 714 ASP cc_start: 0.2536 (m-30) cc_final: 0.2116 (t0) REVERT: E 155 PHE cc_start: 0.3876 (m-80) cc_final: 0.3642 (m-80) REVERT: E 320 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8229 (mm-30) REVERT: E 689 MET cc_start: 0.6200 (ppp) cc_final: 0.5898 (ppp) outliers start: 53 outliers final: 37 residues processed: 211 average time/residue: 0.1723 time to fit residues: 60.6534 Evaluate side-chains 199 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 267 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 412 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 HIS D 332 ASN D 560 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS E 527 HIS ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.144833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095924 restraints weight = 75337.020| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.36 r_work: 0.3164 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34122 Z= 0.266 Angle : 0.644 13.945 46326 Z= 0.317 Chirality : 0.042 0.235 5166 Planarity : 0.005 0.059 6186 Dihedral : 4.075 36.212 4800 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 11.77 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.78 (0.13), residues: 4302 helix: 1.52 (0.11), residues: 2232 sheet: -1.02 (0.22), residues: 525 loop : -0.28 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 34 TYR 0.026 0.002 TYR C 50 PHE 0.023 0.002 PHE C 629 TRP 0.014 0.002 TRP E 205 HIS 0.007 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00616 (34122) covalent geometry : angle 0.64440 (46326) hydrogen bonds : bond 0.03893 ( 1830) hydrogen bonds : angle 4.37511 ( 5292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 86 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7359 (ttp-170) REVERT: D 287 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.7838 (mmm160) REVERT: D 498 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7588 (mt-10) REVERT: D 688 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.7917 (tpt90) REVERT: D 689 MET cc_start: 0.7010 (mmt) cc_final: 0.6775 (mmp) REVERT: C 57 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8725 (tt) REVERT: C 124 PHE cc_start: 0.5870 (t80) cc_final: 0.5149 (t80) REVERT: C 128 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8775 (pttp) REVERT: C 132 GLU cc_start: 0.8379 (tt0) cc_final: 0.8133 (tm-30) REVERT: B 40 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: B 646 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8725 (pp) REVERT: B 651 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 245 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3100 (mt) REVERT: A 356 MET cc_start: 0.3730 (pmm) cc_final: 0.2943 (pmm) REVERT: A 372 GLU cc_start: 0.7816 (mp0) cc_final: 0.7328 (pt0) REVERT: A 385 GLU cc_start: 0.4772 (tt0) cc_final: 0.4421 (pt0) REVERT: A 405 LEU cc_start: 0.8531 (mt) cc_final: 0.8172 (mt) REVERT: F 426 MET cc_start: 0.1185 (ptm) cc_final: 0.0916 (tmm) REVERT: F 433 MET cc_start: 0.5395 (ppp) cc_final: 0.5141 (ptm) REVERT: F 533 ARG cc_start: 0.2875 (mtt-85) cc_final: 0.2608 (ptm160) REVERT: F 708 ARG cc_start: 0.5527 (mmp80) cc_final: 0.4931 (tmt170) REVERT: F 714 ASP cc_start: 0.2831 (m-30) cc_final: 0.2375 (t0) REVERT: E 155 PHE cc_start: 0.3781 (m-80) cc_final: 0.3455 (m-80) REVERT: E 320 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 689 MET cc_start: 0.6328 (ppp) cc_final: 0.6111 (ppp) outliers start: 81 outliers final: 57 residues processed: 225 average time/residue: 0.2303 time to fit residues: 84.8197 Evaluate side-chains 214 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 205 TRP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 695 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 146 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 406 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 375 optimal weight: 20.0000 chunk 300 optimal weight: 30.0000 chunk 36 optimal weight: 0.4980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.145923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097361 restraints weight = 76498.767| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.57 r_work: 0.3190 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34122 Z= 0.176 Angle : 0.569 14.211 46326 Z= 0.278 Chirality : 0.039 0.242 5166 Planarity : 0.004 0.050 6186 Dihedral : 3.948 35.360 4800 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 12.35 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.87 (0.13), residues: 4302 helix: 1.60 (0.11), residues: 2230 sheet: -0.96 (0.22), residues: 525 loop : -0.26 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 520 TYR 0.025 0.002 TYR B 575 PHE 0.015 0.001 PHE E 119 TRP 0.013 0.001 TRP F 250 HIS 0.005 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00402 (34122) covalent geometry : angle 0.56917 (46326) hydrogen bonds : bond 0.03646 ( 1830) hydrogen bonds : angle 4.23089 ( 5292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 160 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7260 (ptm160) REVERT: D 287 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.7866 (mmm160) REVERT: D 498 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 574 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8524 (m-40) REVERT: D 688 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.7947 (tpt90) REVERT: D 689 MET cc_start: 0.7027 (mmt) cc_final: 0.6760 (mmp) REVERT: C 57 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 119 PHE cc_start: 0.7848 (m-80) cc_final: 0.7641 (m-80) REVERT: C 124 PHE cc_start: 0.5818 (t80) cc_final: 0.5134 (t80) REVERT: C 128 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8829 (pttp) REVERT: C 132 GLU cc_start: 0.8384 (tt0) cc_final: 0.8142 (tm-30) REVERT: C 207 LEU cc_start: 0.8339 (mt) cc_final: 0.8090 (pp) REVERT: B 40 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8346 (tp30) REVERT: B 646 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8734 (pp) REVERT: B 651 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 245 LEU cc_start: 0.3856 (OUTLIER) cc_final: 0.3187 (mt) REVERT: A 385 GLU cc_start: 0.4827 (tt0) cc_final: 0.4487 (pt0) REVERT: A 405 LEU cc_start: 0.8507 (mt) cc_final: 0.8139 (mt) REVERT: F 426 MET cc_start: 0.1259 (ptm) cc_final: 0.0990 (tmm) REVERT: F 433 MET cc_start: 0.5534 (ppp) cc_final: 0.4733 (ptm) REVERT: F 533 ARG cc_start: 0.2952 (mtt-85) cc_final: 0.2706 (ptm160) REVERT: F 556 ARG cc_start: 0.5011 (mmp80) cc_final: 0.4485 (mmm160) REVERT: F 708 ARG cc_start: 0.5517 (mmp80) cc_final: 0.4903 (tmt170) REVERT: F 714 ASP cc_start: 0.2880 (m-30) cc_final: 0.2480 (t0) REVERT: E 155 PHE cc_start: 0.3391 (m-80) cc_final: 0.3132 (m-80) REVERT: E 320 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8442 (mm-30) outliers start: 68 outliers final: 52 residues processed: 211 average time/residue: 0.2386 time to fit residues: 81.5670 Evaluate side-chains 208 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 205 TRP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 295 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.147493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099171 restraints weight = 76188.081| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.69 r_work: 0.3229 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34122 Z= 0.116 Angle : 0.538 14.781 46326 Z= 0.261 Chirality : 0.039 0.277 5166 Planarity : 0.004 0.047 6186 Dihedral : 3.792 35.047 4800 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 12.59 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 1.04 (0.13), residues: 4302 helix: 1.72 (0.11), residues: 2230 sheet: -0.82 (0.22), residues: 534 loop : -0.17 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 520 TYR 0.029 0.002 TYR B 575 PHE 0.013 0.001 PHE E 119 TRP 0.014 0.001 TRP D 323 HIS 0.004 0.001 HIS E 469 Details of bonding type rmsd covalent geometry : bond 0.00255 (34122) covalent geometry : angle 0.53782 (46326) hydrogen bonds : bond 0.03438 ( 1830) hydrogen bonds : angle 4.08559 ( 5292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (tt) REVERT: D 86 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7438 (ttp-170) REVERT: D 287 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.7893 (mmm160) REVERT: D 498 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7641 (mt-10) REVERT: D 688 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.7969 (tpt90) REVERT: C 57 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8673 (tt) REVERT: C 124 PHE cc_start: 0.5756 (t80) cc_final: 0.5003 (t80) REVERT: C 128 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8767 (pttp) REVERT: C 132 GLU cc_start: 0.8335 (tt0) cc_final: 0.7993 (tm-30) REVERT: C 207 LEU cc_start: 0.8325 (mt) cc_final: 0.8086 (pp) REVERT: C 688 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7586 (mmm-85) REVERT: B 40 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: B 646 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 651 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 245 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3300 (mt) REVERT: A 385 GLU cc_start: 0.4979 (tt0) cc_final: 0.4603 (pt0) REVERT: A 405 LEU cc_start: 0.8499 (mt) cc_final: 0.8121 (mt) REVERT: F 144 GLU cc_start: 0.4774 (pp20) cc_final: 0.4101 (mm-30) REVERT: F 426 MET cc_start: 0.1314 (ptm) cc_final: 0.0988 (tmm) REVERT: F 433 MET cc_start: 0.5651 (ppp) cc_final: 0.4857 (ptm) REVERT: F 533 ARG cc_start: 0.3067 (mtt-85) cc_final: 0.2815 (ptm160) REVERT: F 556 ARG cc_start: 0.5176 (mmp80) cc_final: 0.4701 (mmm160) REVERT: F 689 MET cc_start: 0.2730 (OUTLIER) cc_final: 0.0579 (tmm) REVERT: F 708 ARG cc_start: 0.5434 (mmp80) cc_final: 0.4832 (tmt170) REVERT: F 714 ASP cc_start: 0.2821 (m-30) cc_final: 0.2402 (t0) REVERT: E 139 ARG cc_start: 0.6962 (ttt180) cc_final: 0.6342 (mmm-85) REVERT: E 204 ASP cc_start: 0.9026 (m-30) cc_final: 0.8453 (p0) REVERT: E 320 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8478 (mm-30) REVERT: E 520 ARG cc_start: 0.2899 (ptp90) cc_final: 0.2394 (mpp-170) outliers start: 60 outliers final: 41 residues processed: 218 average time/residue: 0.2332 time to fit residues: 83.0942 Evaluate side-chains 206 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 414 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 392 optimal weight: 0.0470 chunk 372 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 HIS E 355 GLN E 612 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.143662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092493 restraints weight = 75727.946| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.02 r_work: 0.3148 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 34122 Z= 0.326 Angle : 0.714 15.355 46326 Z= 0.351 Chirality : 0.044 0.402 5166 Planarity : 0.005 0.056 6186 Dihedral : 4.217 35.416 4800 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.76 % Allowed : 12.82 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.63 (0.13), residues: 4302 helix: 1.37 (0.11), residues: 2228 sheet: -1.00 (0.21), residues: 546 loop : -0.34 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 520 TYR 0.029 0.002 TYR C 50 PHE 0.025 0.002 PHE C 629 TRP 0.023 0.002 TRP E 205 HIS 0.006 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00751 (34122) covalent geometry : angle 0.71394 (46326) hydrogen bonds : bond 0.04086 ( 1830) hydrogen bonds : angle 4.53168 ( 5292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7607 (ttm170) REVERT: D 287 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.7838 (mmm160) REVERT: D 498 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7642 (mt-10) REVERT: D 688 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.7954 (tpt90) REVERT: D 689 MET cc_start: 0.7084 (mmt) cc_final: 0.6831 (mmp) REVERT: C 57 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8737 (tt) REVERT: C 124 PHE cc_start: 0.5828 (t80) cc_final: 0.4293 (t80) REVERT: C 128 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8339 (mmtm) REVERT: C 132 GLU cc_start: 0.8421 (tt0) cc_final: 0.8106 (tm-30) REVERT: C 201 LEU cc_start: 0.8600 (pt) cc_final: 0.8123 (pt) REVERT: B 40 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: B 646 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8764 (pp) REVERT: A 245 LEU cc_start: 0.4002 (OUTLIER) cc_final: 0.3363 (mt) REVERT: A 405 LEU cc_start: 0.8458 (mt) cc_final: 0.8115 (mt) REVERT: F 140 GLU cc_start: 0.5979 (mt-10) cc_final: 0.4995 (tm-30) REVERT: F 433 MET cc_start: 0.5554 (ppp) cc_final: 0.4733 (ptm) REVERT: F 533 ARG cc_start: 0.3092 (mtt-85) cc_final: 0.2859 (ptm160) REVERT: F 543 HIS cc_start: 0.4207 (m170) cc_final: 0.3954 (m-70) REVERT: F 556 ARG cc_start: 0.4831 (mmp80) cc_final: 0.4248 (mmm160) REVERT: F 689 MET cc_start: 0.2831 (OUTLIER) cc_final: 0.0517 (tmm) REVERT: F 708 ARG cc_start: 0.5493 (mmp80) cc_final: 0.4827 (tmt170) REVERT: F 714 ASP cc_start: 0.2818 (m-30) cc_final: 0.2397 (t0) REVERT: E 320 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8428 (mm-30) outliers start: 60 outliers final: 47 residues processed: 207 average time/residue: 0.2341 time to fit residues: 79.4366 Evaluate side-chains 200 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 557 TYR Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 689 MET Chi-restraints excluded: chain E residue 205 TRP Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 543 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 356 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 329 optimal weight: 30.0000 chunk 138 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 417 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 402 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.146079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096544 restraints weight = 76424.379| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.36 r_work: 0.3200 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34122 Z= 0.141 Angle : 0.583 14.931 46326 Z= 0.283 Chirality : 0.040 0.402 5166 Planarity : 0.004 0.061 6186 Dihedral : 3.968 36.201 4800 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 1.56 % Allowed : 13.26 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.81 (0.13), residues: 4302 helix: 1.54 (0.11), residues: 2234 sheet: -0.92 (0.22), residues: 537 loop : -0.30 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 199 TYR 0.028 0.002 TYR B 575 PHE 0.014 0.001 PHE D 571 TRP 0.017 0.001 TRP F 250 HIS 0.004 0.001 HIS E 469 Details of bonding type rmsd covalent geometry : bond 0.00318 (34122) covalent geometry : angle 0.58327 (46326) hydrogen bonds : bond 0.03609 ( 1830) hydrogen bonds : angle 4.24717 ( 5292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9504.73 seconds wall clock time: 162 minutes 53.86 seconds (9773.86 seconds total)