Starting phenix.real_space_refine on Sat Jun 28 19:45:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8w_36966/06_2025/8k8w_36966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8w_36966/06_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_36966/06_2025/8k8w_36966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8w_36966/06_2025/8k8w_36966.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8w_36966/06_2025/8k8w_36966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8w_36966/06_2025/8k8w_36966.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.28, per 1000 atoms: 0.58 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: 8.54 Conformation dependent library (CDL) restraints added in 4.5 seconds 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: 4.42 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: 13.82 Time building geometry restraints manager: 9.70 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: 0.06 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: 0.010 Normalize map: mean=0, sd=1: 2.320 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: 1.490 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 75.610 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (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 TRP 0.014 0.001 TRP F 10 HIS 0.007 0.001 HIS A 713 PHE 0.016 0.001 PHE C 571 TYR 0.014 0.001 TYR E 271 ARG 0.011 0.000 ARG F 328 Details of bonding type rmsd hydrogen bonds : bond 0.14304 ( 1830) hydrogen bonds : angle 5.25907 ( 5292) covalent geometry : bond 0.00239 (34122) covalent geometry : angle 0.56623 (46326) *********************** 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 : 3.367 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: 0.5177 (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: 0.7646 (tp30) REVERT: A 356 MET cc_start: 0.3418 (pmm) cc_final: 0.3050 (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: 0.4237 (ptm) REVERT: F 632 VAL cc_start: 0.2362 (t) cc_final: 0.2024 (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: 0.4091 (t0) REVERT: E 26 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.7212 (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: 0.5459 time to fit residues: 401.5780 Evaluate side-chains 208 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 3.949 ------------------------------------------------------------------------------- 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 359 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 333 optimal weight: 40.0000 chunk 129 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 386 optimal weight: 0.9980 overall best weight: 1.9382 ------------------------------------------------------------------------------- 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 696 GLN B 141 GLN B 597 ASN B 612 GLN A 97 GLN A 253 ASN A 334 GLN A 462 GLN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105986 restraints weight = 76744.093| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.74 r_work: 0.3362 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34122 Z= 0.152 Angle : 0.580 13.921 46326 Z= 0.288 Chirality : 0.039 0.259 5166 Planarity : 0.005 0.084 6186 Dihedral : 3.984 43.778 4803 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 1.17 % Allowed : 6.31 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.13), residues: 4302 helix: 1.86 (0.11), residues: 2237 sheet: -0.91 (0.22), residues: 509 loop : -0.34 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 205 HIS 0.009 0.001 HIS F 303 PHE 0.033 0.001 PHE E 119 TYR 0.023 0.002 TYR B 575 ARG 0.007 0.001 ARG D 520 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 1830) hydrogen bonds : angle 4.39087 ( 5292) covalent geometry : bond 0.00339 (34122) covalent geometry : angle 0.58030 (46326) *********************** 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 264 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 3.475 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 124 PHE cc_start: 0.6875 (t80) cc_final: 0.5574 (t80) REVERT: D 188 LEU cc_start: 0.8638 (mt) cc_final: 0.8432 (tp) REVERT: D 688 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8023 (tpt-90) REVERT: C 124 PHE cc_start: 0.5755 (t80) cc_final: 0.5285 (t80) REVERT: C 125 LEU cc_start: 0.8642 (mt) cc_final: 0.8366 (mt) REVERT: C 128 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8815 (pttp) REVERT: C 132 GLU cc_start: 0.8115 (tt0) cc_final: 0.7852 (tm-30) REVERT: C 141 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7411 (mt0) REVERT: C 510 TYR cc_start: 0.8144 (p90) cc_final: 0.7933 (p90) REVERT: B 254 LEU cc_start: 0.8343 (mt) cc_final: 0.8111 (pp) REVERT: A 1 MET cc_start: 0.7704 (tmm) cc_final: 0.7379 (ttt) REVERT: A 689 MET cc_start: 0.2274 (mtt) cc_final: 0.1894 (mtt) REVERT: F 15 GLU cc_start: 0.3935 (mm-30) cc_final: 0.2670 (mt-10) REVERT: F 140 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5667 (tm-30) REVERT: F 250 TRP cc_start: 0.6163 (m100) cc_final: 0.5721 (m100) REVERT: F 282 ASP cc_start: 0.4831 (m-30) cc_final: 0.4512 (t0) REVERT: F 433 MET cc_start: 0.5268 (ppp) cc_final: 0.4912 (ptm) REVERT: F 708 ARG cc_start: 0.6025 (mmp80) cc_final: 0.5236 (tmt170) outliers start: 40 outliers final: 17 residues processed: 252 average time/residue: 0.4671 time to fit residues: 191.5895 Evaluate side-chains 174 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 3.463 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain B residue 271 TYR 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 458 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain E residue 205 TRP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 634 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 324 optimal weight: 20.0000 chunk 409 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 220 optimal weight: 30.0000 chunk 349 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 254 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN D 560 HIS C 60 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 483 GLN B 653 ASN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN F 543 HIS F 650 ASN F 653 ASN F 679 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.144387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095296 restraints weight = 75306.128| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.49 r_work: 0.3158 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 34122 Z= 0.339 Angle : 0.736 10.414 46326 Z= 0.366 Chirality : 0.044 0.196 5166 Planarity : 0.006 0.100 6186 Dihedral : 4.375 39.137 4800 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 1.85 % Allowed : 8.57 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4302 helix: 1.33 (0.11), residues: 2222 sheet: -1.23 (0.21), residues: 523 loop : -0.50 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 323 HIS 0.010 0.002 HIS C 208 PHE 0.027 0.002 PHE F 542 TYR 0.030 0.003 TYR B 50 ARG 0.015 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1830) hydrogen bonds : angle 4.68781 ( 5292) covalent geometry : bond 0.00782 (34122) covalent geometry : angle 0.73599 (46326) *********************** 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 236 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 3.663 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 124 PHE cc_start: 0.6866 (t80) cc_final: 0.5751 (t80) REVERT: D 688 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.7866 (tpt90) REVERT: D 689 MET cc_start: 0.6990 (mmt) cc_final: 0.6603 (mmp) REVERT: C 57 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 124 PHE cc_start: 0.5904 (t80) cc_final: 0.5310 (t80) REVERT: C 125 LEU cc_start: 0.8705 (mt) cc_final: 0.8504 (mt) REVERT: C 128 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8826 (pttp) REVERT: C 132 GLU cc_start: 0.8311 (tt0) cc_final: 0.8048 (tm-30) REVERT: B 40 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: B 86 ARG cc_start: 0.8103 (mpt180) cc_final: 0.7708 (mtt90) REVERT: B 363 THR cc_start: 0.8292 (p) cc_final: 0.8035 (t) REVERT: B 646 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8777 (pp) REVERT: B 689 MET cc_start: 0.6134 (mpp) cc_final: 0.5928 (mmm) REVERT: F 140 GLU cc_start: 0.6524 (mt-10) cc_final: 0.5701 (tm-30) REVERT: F 250 TRP cc_start: 0.6144 (m100) cc_final: 0.5878 (m100) REVERT: F 433 MET cc_start: 0.5164 (ppp) cc_final: 0.4891 (ptm) REVERT: F 708 ARG cc_start: 0.5951 (mmp80) cc_final: 0.5220 (tmt170) REVERT: E 119 PHE cc_start: 0.7714 (m-80) cc_final: 0.6608 (m-80) REVERT: E 155 PHE cc_start: 0.4205 (m-80) cc_final: 0.3980 (m-80) REVERT: E 356 MET cc_start: 0.8922 (ptt) cc_final: 0.8673 (ptt) outliers start: 63 outliers final: 40 residues processed: 221 average time/residue: 0.4596 time to fit residues: 168.5586 Evaluate side-chains 189 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 3.685 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain D residue 426 MET 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 496 VAL Chi-restraints excluded: chain B residue 40 GLU 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 B residue 347 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 532 ASP 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 458 GLU 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 194 LEU 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 543 HIS Chi-restraints excluded: chain E residue 634 LYS Chi-restraints excluded: chain E residue 695 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 370 optimal weight: 0.1980 chunk 253 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 338 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 208 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** F 151 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 = 0.4320 r_free = 0.4320 target = 0.148120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098972 restraints weight = 76581.035| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 4.47 r_work: 0.3243 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2505 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= 0.113 Angle : 0.536 10.508 46326 Z= 0.265 Chirality : 0.038 0.216 5166 Planarity : 0.004 0.046 6186 Dihedral : 3.984 38.768 4800 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 1.58 % Allowed : 10.04 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4302 helix: 1.63 (0.11), residues: 2227 sheet: -0.97 (0.22), residues: 519 loop : -0.36 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 323 HIS 0.009 0.001 HIS B 560 PHE 0.015 0.001 PHE E 119 TYR 0.020 0.002 TYR B 575 ARG 0.006 0.000 ARG F 328 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1830) hydrogen bonds : angle 4.23062 ( 5292) covalent geometry : bond 0.00240 (34122) covalent geometry : angle 0.53566 (46326) *********************** 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 241 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 3.345 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 86 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7520 (ttp-170) REVERT: D 200 ARG cc_start: 0.8910 (ptt-90) cc_final: 0.8624 (ptt-90) REVERT: D 201 LEU cc_start: 0.9014 (tp) cc_final: 0.8709 (pp) REVERT: D 688 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.7907 (tpt90) REVERT: D 689 MET cc_start: 0.6850 (mmt) cc_final: 0.6572 (mmp) REVERT: C 124 PHE cc_start: 0.5851 (t80) cc_final: 0.5254 (t80) REVERT: C 128 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8771 (pttp) REVERT: C 132 GLU cc_start: 0.8363 (tt0) cc_final: 0.8062 (tm-30) REVERT: B 86 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7652 (mtt90) REVERT: B 689 MET cc_start: 0.6203 (mpp) cc_final: 0.5988 (mmm) REVERT: F 140 GLU cc_start: 0.6458 (mt-10) cc_final: 0.5649 (tm-30) REVERT: F 282 ASP cc_start: 0.5051 (m-30) cc_final: 0.4502 (t0) REVERT: F 433 MET cc_start: 0.5299 (ppp) cc_final: 0.4931 (ptm) REVERT: F 708 ARG cc_start: 0.5851 (mmp80) cc_final: 0.5163 (tmt170) REVERT: E 155 PHE cc_start: 0.4007 (m-80) cc_final: 0.3724 (m-80) outliers start: 54 outliers final: 28 residues processed: 223 average time/residue: 0.4415 time to fit residues: 163.1394 Evaluate side-chains 183 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL 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 695 LEU Chi-restraints excluded: chain B residue 217 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 419 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 VAL 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 661 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 332 ASN Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 634 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 30.0000 chunk 364 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 379 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN B 48 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN F 211 ASN F 543 HIS F 602 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093207 restraints weight = 75637.523| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.26 r_work: 0.3131 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 34122 Z= 0.382 Angle : 0.767 13.472 46326 Z= 0.379 Chirality : 0.045 0.232 5166 Planarity : 0.006 0.064 6186 Dihedral : 4.435 38.994 4800 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 2.17 % Allowed : 11.15 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4302 helix: 1.20 (0.11), residues: 2229 sheet: -0.99 (0.23), residues: 483 loop : -0.58 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 205 HIS 0.009 0.002 HIS D 48 PHE 0.025 0.002 PHE C 629 TYR 0.031 0.003 TYR C 50 ARG 0.011 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1830) hydrogen bonds : angle 4.69349 ( 5292) covalent geometry : bond 0.00889 (34122) covalent geometry : angle 0.76727 (46326) *********************** 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 233 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 159 time to evaluate : 3.497 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: D 688 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.7965 (tpt90) REVERT: D 689 MET cc_start: 0.7002 (mmt) cc_final: 0.6775 (mmp) REVERT: C 57 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 124 PHE cc_start: 0.5981 (t80) cc_final: 0.5335 (t80) REVERT: C 128 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8824 (pttp) REVERT: C 132 GLU cc_start: 0.8401 (tt0) cc_final: 0.8159 (tm-30) REVERT: B 40 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: B 646 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8827 (pp) REVERT: A 425 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8836 (tpt-90) REVERT: F 433 MET cc_start: 0.5371 (ppp) cc_final: 0.4570 (ptm) REVERT: F 708 ARG cc_start: 0.5668 (mmp80) cc_final: 0.5046 (tmt170) REVERT: E 1 MET cc_start: 0.8784 (ppp) cc_final: 0.8545 (ppp) REVERT: E 119 PHE cc_start: 0.7690 (m-80) cc_final: 0.6718 (m-80) REVERT: E 689 MET cc_start: 0.6301 (ppp) cc_final: 0.5981 (ppp) outliers start: 74 outliers final: 43 residues processed: 213 average time/residue: 0.5309 time to fit residues: 191.7930 Evaluate side-chains 191 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 THR 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 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 342 GLN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 217 LEU 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 639 SER 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 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 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 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 695 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 145 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 358 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 237 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.146081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096710 restraints weight = 76537.596| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.20 r_work: 0.3207 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34122 Z= 0.142 Angle : 0.568 12.748 46326 Z= 0.277 Chirality : 0.039 0.330 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.066 38.642 4800 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.88 % Favored : 97.09 % Rotamer: Outliers : 1.82 % Allowed : 12.06 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 4302 helix: 1.50 (0.11), residues: 2227 sheet: -0.86 (0.23), residues: 484 loop : -0.47 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 323 HIS 0.007 0.001 HIS C 208 PHE 0.016 0.001 PHE B 630 TYR 0.021 0.002 TYR B 575 ARG 0.005 0.000 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1830) hydrogen bonds : angle 4.29392 ( 5292) covalent geometry : bond 0.00318 (34122) covalent geometry : angle 0.56816 (46326) *********************** 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 227 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 3.473 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: 0.9101 (OUTLIER) cc_final: 0.8635 (tt) REVERT: D 201 LEU cc_start: 0.9057 (tp) cc_final: 0.8766 (pp) REVERT: D 688 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.7981 (tpt90) REVERT: D 689 MET cc_start: 0.7010 (mmt) cc_final: 0.6768 (mmp) REVERT: C 124 PHE cc_start: 0.5939 (t80) cc_final: 0.5312 (t80) REVERT: C 128 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8765 (pttp) REVERT: C 132 GLU cc_start: 0.8369 (tt0) cc_final: 0.8060 (tm-30) REVERT: B 86 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7572 (mtt90) REVERT: B 651 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 385 GLU cc_start: 0.4500 (tt0) cc_final: 0.3998 (pt0) REVERT: A 425 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8835 (tpt-90) REVERT: F 255 LEU cc_start: 0.6703 (mt) cc_final: 0.6467 (mp) REVERT: F 433 MET cc_start: 0.5409 (ppp) cc_final: 0.4621 (ptm) REVERT: F 708 ARG cc_start: 0.5660 (mmp80) cc_final: 0.5026 (tmt170) REVERT: E 119 PHE cc_start: 0.7613 (m-80) cc_final: 0.6634 (m-80) REVERT: E 155 PHE cc_start: 0.3559 (m-80) cc_final: 0.3299 (m-80) outliers start: 62 outliers final: 38 residues processed: 209 average time/residue: 0.4784 time to fit residues: 167.3411 Evaluate side-chains 193 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 110 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 426 MET 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 342 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 217 LEU 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 623 ASN Chi-restraints excluded: chain B residue 639 SER 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 386 PHE Chi-restraints excluded: chain A residue 425 ARG 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 105 VAL 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 80 optimal weight: 5.9990 chunk 396 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 382 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 264 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 151 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 = 0.4296 r_free = 0.4296 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097482 restraints weight = 75001.090| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.25 r_work: 0.3211 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34122 Z= 0.151 Angle : 0.558 13.036 46326 Z= 0.272 Chirality : 0.039 0.234 5166 Planarity : 0.004 0.049 6186 Dihedral : 3.949 37.980 4800 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 2.05 % Allowed : 11.97 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4302 helix: 1.58 (0.11), residues: 2227 sheet: -0.96 (0.22), residues: 523 loop : -0.35 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 323 HIS 0.004 0.001 HIS E 469 PHE 0.015 0.001 PHE C 629 TYR 0.026 0.002 TYR B 575 ARG 0.005 0.000 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1830) hydrogen bonds : angle 4.20870 ( 5292) covalent geometry : bond 0.00341 (34122) covalent geometry : angle 0.55836 (46326) *********************** 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 231 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 4.053 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 57 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8647 (tt) REVERT: D 86 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7289 (ttp-170) REVERT: D 603 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: D 688 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7954 (tpt90) REVERT: C 124 PHE cc_start: 0.5892 (t80) cc_final: 0.5175 (t80) REVERT: C 128 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8773 (pttp) REVERT: B 86 ARG cc_start: 0.7940 (mpt180) cc_final: 0.7514 (mtt90) REVERT: B 651 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 245 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3228 (mt) REVERT: A 385 GLU cc_start: 0.4590 (tt0) cc_final: 0.4034 (pt0) REVERT: F 255 LEU cc_start: 0.6660 (mt) cc_final: 0.6419 (mp) REVERT: F 433 MET cc_start: 0.5403 (ppp) cc_final: 0.5136 (ptm) REVERT: F 533 ARG cc_start: 0.2906 (mtt-85) cc_final: 0.2617 (ptm160) REVERT: F 708 ARG cc_start: 0.5562 (mmp80) cc_final: 0.4964 (tmt170) REVERT: E 119 PHE cc_start: 0.7578 (m-80) cc_final: 0.6563 (m-80) REVERT: E 155 PHE cc_start: 0.3653 (m-80) cc_final: 0.3395 (m-80) REVERT: E 689 MET cc_start: 0.6160 (ppp) cc_final: 0.5736 (ppp) outliers start: 70 outliers final: 51 residues processed: 209 average time/residue: 0.5510 time to fit residues: 194.3197 Evaluate side-chains 208 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 249 GLN 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 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 603 ASP Chi-restraints excluded: chain D residue 613 THR 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 C residue 695 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 254 LEU 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 505 VAL Chi-restraints excluded: chain B residue 623 ASN 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 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 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 105 VAL Chi-restraints excluded: chain E residue 194 LEU 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 543 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 387 optimal weight: 6.9990 chunk 374 optimal weight: 30.0000 chunk 421 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 407 optimal weight: 20.0000 chunk 332 optimal weight: 0.0570 overall best weight: 2.0902 ------------------------------------------------------------------------------- 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 ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 151 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 = 0.4305 r_free = 0.4305 target = 0.146832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098643 restraints weight = 76391.251| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.74 r_work: 0.3203 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34122 Z= 0.144 Angle : 0.550 14.481 46326 Z= 0.266 Chirality : 0.038 0.218 5166 Planarity : 0.004 0.052 6186 Dihedral : 3.875 37.245 4800 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.94 % Allowed : 12.09 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 4302 helix: 1.64 (0.11), residues: 2228 sheet: -0.86 (0.22), residues: 533 loop : -0.30 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 290 HIS 0.004 0.001 HIS C 208 PHE 0.014 0.001 PHE C 119 TYR 0.028 0.002 TYR B 575 ARG 0.004 0.000 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1830) hydrogen bonds : angle 4.15898 ( 5292) covalent geometry : bond 0.00326 (34122) covalent geometry : angle 0.54976 (46326) *********************** 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 230 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 3.718 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: 0.7590 (ptm160) cc_final: 0.7284 (ttp-170) REVERT: D 574 ASN cc_start: 0.8753 (p0) cc_final: 0.8527 (m-40) REVERT: D 603 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: D 688 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.7980 (tpt90) REVERT: D 689 MET cc_start: 0.7016 (mmt) cc_final: 0.6743 (mmp) REVERT: C 124 PHE cc_start: 0.5818 (t80) cc_final: 0.5162 (t80) REVERT: C 128 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8827 (pttp) REVERT: C 132 GLU cc_start: 0.8370 (tt0) cc_final: 0.8096 (tm-30) REVERT: B 86 ARG cc_start: 0.7939 (mpt180) cc_final: 0.7504 (mtt90) REVERT: B 646 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8771 (pp) REVERT: B 651 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 245 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3097 (mt) REVERT: A 385 GLU cc_start: 0.4654 (tt0) cc_final: 0.4106 (pt0) REVERT: F 255 LEU cc_start: 0.6653 (mt) cc_final: 0.6417 (mp) REVERT: F 433 MET cc_start: 0.5542 (ppp) cc_final: 0.5274 (ptm) REVERT: F 533 ARG cc_start: 0.2909 (mtt-85) cc_final: 0.2650 (ptm160) REVERT: F 689 MET cc_start: 0.3115 (OUTLIER) cc_final: 0.0529 (ttp) REVERT: F 708 ARG cc_start: 0.5514 (mmp80) cc_final: 0.4908 (tmt170) REVERT: E 119 PHE cc_start: 0.7569 (m-80) cc_final: 0.6531 (m-80) REVERT: E 689 MET cc_start: 0.6198 (ppp) cc_final: 0.5885 (ppp) outliers start: 66 outliers final: 55 residues processed: 211 average time/residue: 0.5829 time to fit residues: 207.9473 Evaluate side-chains 211 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 LEU 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 332 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 613 THR 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 C residue 695 LEU 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 217 LEU Chi-restraints excluded: chain B residue 254 LEU 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 505 VAL Chi-restraints excluded: chain B residue 623 ASN Chi-restraints excluded: chain B residue 639 SER 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 585 LEU 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 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 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 105 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 492 THR 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 255 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 355 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 HIS E 355 GLN E 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.143341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094586 restraints weight = 75271.177| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.06 r_work: 0.3152 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 34122 Z= 0.317 Angle : 0.701 15.027 46326 Z= 0.344 Chirality : 0.043 0.209 5166 Planarity : 0.005 0.050 6186 Dihedral : 4.252 36.619 4800 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 2.14 % Allowed : 12.35 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 4302 helix: 1.32 (0.11), residues: 2224 sheet: -0.81 (0.23), residues: 489 loop : -0.46 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 205 HIS 0.007 0.001 HIS D 48 PHE 0.024 0.002 PHE C 629 TYR 0.027 0.002 TYR C 50 ARG 0.009 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 1830) hydrogen bonds : angle 4.53947 ( 5292) covalent geometry : bond 0.00734 (34122) covalent geometry : angle 0.70086 (46326) *********************** 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 231 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 158 time to evaluate : 4.643 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: D 603 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: D 688 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.7991 (tpt90) REVERT: D 689 MET cc_start: 0.7226 (mmt) cc_final: 0.6942 (mmp) REVERT: C 124 PHE cc_start: 0.5871 (t80) cc_final: 0.5138 (t80) REVERT: C 132 GLU cc_start: 0.8395 (tt0) cc_final: 0.8084 (tm-30) REVERT: B 40 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: B 86 ARG cc_start: 0.8060 (mpt180) cc_final: 0.7652 (mtt90) REVERT: B 646 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8764 (pp) REVERT: B 690 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6650 (pm20) REVERT: A 245 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3211 (mt) REVERT: F 250 TRP cc_start: 0.5858 (m100) cc_final: 0.5558 (m100) REVERT: F 433 MET cc_start: 0.5542 (ppp) cc_final: 0.5286 (ptm) REVERT: F 533 ARG cc_start: 0.2984 (mtt-85) cc_final: 0.2767 (ptm160) REVERT: F 543 HIS cc_start: 0.4144 (m170) cc_final: 0.3878 (m-70) REVERT: F 556 ARG cc_start: 0.4804 (mmp80) cc_final: 0.4228 (mmm160) REVERT: F 708 ARG cc_start: 0.5520 (mmp80) cc_final: 0.4854 (tmt170) REVERT: E 119 PHE cc_start: 0.7594 (m-80) cc_final: 0.6564 (m-80) REVERT: E 689 MET cc_start: 0.6356 (ppp) cc_final: 0.6106 (ppp) outliers start: 73 outliers final: 53 residues processed: 211 average time/residue: 0.7075 time to fit residues: 246.6247 Evaluate side-chains 206 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 3.497 ------------------------------------------------------------------------------- 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 576 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 254 LEU 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 505 VAL Chi-restraints excluded: chain B residue 639 SER 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 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 105 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 492 THR 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 330 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 147 optimal weight: 0.0570 chunk 238 optimal weight: 8.9990 chunk 400 optimal weight: 20.0000 chunk 425 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 395 optimal weight: 0.8980 chunk 383 optimal weight: 6.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 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 = 0.4300 r_free = 0.4300 target = 0.146471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097194 restraints weight = 76327.493| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.33 r_work: 0.3203 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34122 Z= 0.135 Angle : 0.570 15.462 46326 Z= 0.276 Chirality : 0.039 0.237 5166 Planarity : 0.004 0.055 6186 Dihedral : 4.002 37.163 4800 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 1.94 % Allowed : 12.71 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.13), residues: 4302 helix: 1.52 (0.11), residues: 2224 sheet: -0.92 (0.22), residues: 533 loop : -0.31 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 323 HIS 0.004 0.001 HIS E 469 PHE 0.015 0.001 PHE D 571 TYR 0.029 0.002 TYR B 575 ARG 0.006 0.000 ARG E 520 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1830) hydrogen bonds : angle 4.24875 ( 5292) covalent geometry : bond 0.00299 (34122) covalent geometry : angle 0.56994 (46326) ********************** 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 226 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 4.810 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 86 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7351 (ptm160) REVERT: D 201 LEU cc_start: 0.9036 (tp) cc_final: 0.8702 (pp) REVERT: D 688 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.7929 (tpt90) REVERT: D 689 MET cc_start: 0.7098 (mmt) cc_final: 0.6839 (mmp) REVERT: C 119 PHE cc_start: 0.7848 (m-80) cc_final: 0.7624 (m-80) REVERT: C 124 PHE cc_start: 0.5803 (t80) cc_final: 0.5022 (t80) REVERT: C 128 LYS cc_start: 0.9123 (ttpp) cc_final: 0.8825 (pttp) REVERT: B 86 ARG cc_start: 0.7910 (mpt180) cc_final: 0.7486 (mtt90) REVERT: B 282 ASP cc_start: 0.7335 (m-30) cc_final: 0.7121 (m-30) REVERT: B 356 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8901 (ptm) REVERT: B 646 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 651 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 690 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6746 (pm20) REVERT: A 245 LEU cc_start: 0.4014 (OUTLIER) cc_final: 0.3121 (mt) REVERT: F 433 MET cc_start: 0.5546 (ppp) cc_final: 0.4739 (ptm) REVERT: F 556 ARG cc_start: 0.4912 (mmp80) cc_final: 0.4491 (mmt180) REVERT: F 689 MET cc_start: 0.2795 (OUTLIER) cc_final: 0.0592 (tmm) REVERT: F 708 ARG cc_start: 0.5445 (mmp80) cc_final: 0.4817 (tmt170) REVERT: E 119 PHE cc_start: 0.7551 (m-80) cc_final: 0.6491 (m-80) REVERT: E 520 ARG cc_start: 0.3319 (mpp80) cc_final: 0.2894 (mpp80) REVERT: E 689 MET cc_start: 0.6233 (ppp) cc_final: 0.5953 (ppp) outliers start: 66 outliers final: 55 residues processed: 210 average time/residue: 0.6667 time to fit residues: 231.8824 Evaluate side-chains 216 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 163 ARG 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 293 ASN 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 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 C residue 695 LEU 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 217 LEU Chi-restraints excluded: chain B residue 254 LEU 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 479 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 639 SER 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 541 ILE Chi-restraints excluded: chain A residue 585 LEU 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 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 105 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 492 THR 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 309 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 291 optimal weight: 40.0000 chunk 392 optimal weight: 0.0570 chunk 208 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 151 optimal weight: 10.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.146929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098593 restraints weight = 76582.202| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.64 r_work: 0.3220 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34122 Z= 0.120 Angle : 0.545 15.027 46326 Z= 0.264 Chirality : 0.038 0.216 5166 Planarity : 0.004 0.049 6186 Dihedral : 3.798 36.662 4800 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 1.85 % Allowed : 12.91 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.13), residues: 4302 helix: 1.65 (0.11), residues: 2228 sheet: -0.82 (0.22), residues: 533 loop : -0.25 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 323 HIS 0.004 0.001 HIS D 713 PHE 0.014 0.001 PHE B 629 TYR 0.026 0.002 TYR B 575 ARG 0.010 0.000 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1830) hydrogen bonds : angle 4.11639 ( 5292) covalent geometry : bond 0.00268 (34122) covalent geometry : angle 0.54454 (46326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20637.81 seconds wall clock time: 360 minutes 50.88 seconds (21650.88 seconds total)