Starting phenix.real_space_refine on Fri Mar 6 22:08:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nib_12353/03_2026/7nib_12353.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 22360 2.51 5 N 5958 2.21 5 O 6609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5055 Classifications: {'peptide': 651} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 625} Chain breaks: 3 Chain: "B" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4251 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 528} Chain breaks: 3 Chain: "C" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4255 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 529} Chain breaks: 3 Chain: "D" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5055 Classifications: {'peptide': 651} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 625} Chain breaks: 3 Chain: "E" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3977 Classifications: {'peptide': 518} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 3 Chain: "F" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3938 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 3 Chain: "G" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4251 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 528} Chain breaks: 3 Chain: "H" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4255 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 529} Chain breaks: 3 Time building chain proxies: 8.60, per 1000 atoms: 0.25 Number of scatterers: 35037 At special positions: 0 Unit cell: (160.383, 164.538, 168.693, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 6609 8.00 N 5958 7.00 C 22360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8438 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 32 sheets defined 48.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.872A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.935A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.517A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.734A pdb=" N GLU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 removed outlier: 3.650A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 removed outlier: 4.178A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.008A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.885A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.542A pdb=" N GLY A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.553A pdb=" N MET A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.235A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.523A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 220 removed outlier: 4.023A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.592A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 removed outlier: 3.605A pdb=" N ALA B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 450 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.029A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.590A pdb=" N ILE B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.674A pdb=" N GLY B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 623 through 636 Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.500A pdb=" N ILE B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 208 through 220 removed outlier: 4.076A pdb=" N LEU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 278 removed outlier: 3.571A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 405 removed outlier: 3.979A pdb=" N ILE C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 450 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.038A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 522 removed outlier: 3.538A pdb=" N ILE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.599A pdb=" N GLY C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 623 through 636 removed outlier: 3.502A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 672 through 686 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.873A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.935A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 266 removed outlier: 3.931A pdb=" N GLN D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 removed outlier: 3.734A pdb=" N GLU D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 367 removed outlier: 3.650A pdb=" N SER D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 403 removed outlier: 4.178A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 450 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.009A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.886A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 570 through 575 removed outlier: 3.542A pdb=" N GLY D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 615 through 621 removed outlier: 3.554A pdb=" N MET D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.236A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.524A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.512A pdb=" N LYS E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 4.016A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 266 removed outlier: 3.528A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 450 Processing helix chain 'E' and resid 457 through 465 removed outlier: 3.975A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 570 through 575 removed outlier: 3.616A pdb=" N GLY E 575 " --> pdb=" O HIS E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.381A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.651A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.937A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 261 removed outlier: 3.620A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 457 through 465 removed outlier: 3.945A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.589A pdb=" N ILE F 510 " --> pdb=" O ALA F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 570 through 575 removed outlier: 3.597A pdb=" N GLY F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 615 through 621 Processing helix chain 'F' and resid 623 through 636 Processing helix chain 'F' and resid 651 through 656 Processing helix chain 'F' and resid 672 through 686 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.545A pdb=" N LYS G 101 " --> pdb=" O MET G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.993A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 264 removed outlier: 3.628A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 429 through 450 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.009A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 570 through 575 removed outlier: 3.658A pdb=" N GLY G 575 " --> pdb=" O HIS G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 587 Processing helix chain 'G' and resid 615 through 621 Processing helix chain 'G' and resid 623 through 636 Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.538A pdb=" N ILE G 676 " --> pdb=" O THR G 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.598A pdb=" N LYS H 101 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 220 removed outlier: 3.976A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.519A pdb=" N HIS H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 429 through 450 Processing helix chain 'H' and resid 457 through 465 removed outlier: 3.922A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 570 through 575 removed outlier: 3.712A pdb=" N GLY H 575 " --> pdb=" O HIS H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 587 Processing helix chain 'H' and resid 615 through 621 Processing helix chain 'H' and resid 623 through 636 Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 657 through 659 No H-bonds generated for 'chain 'H' and resid 657 through 659' Processing helix chain 'H' and resid 672 through 686 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 7.254A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.953A pdb=" N ILE A 137 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN A 192 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 139 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.210A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 643 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 238 removed outlier: 7.035A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 6.784A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 467 through 473 removed outlier: 7.148A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 238 removed outlier: 3.525A pdb=" N ARG C 423 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU C 56 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N ASP C 58 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 13.014A pdb=" N LEU C 60 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 13.392A pdb=" N THR C 417 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 14.422A pdb=" N GLN C 62 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 13.772A pdb=" N ALA C 415 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.935A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 467 through 473 removed outlier: 7.099A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 643 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 7.255A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.953A pdb=" N ILE D 137 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 192 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 139 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.210A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 643 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 221 removed outlier: 6.858A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 141 removed outlier: 5.018A pdb=" N ILE E 137 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN E 192 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 139 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.467A pdb=" N ILE E 472 " --> pdb=" O VAL E 698 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 221 removed outlier: 6.867A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 141 removed outlier: 4.991A pdb=" N ILE F 137 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN F 192 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 139 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.410A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 643 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 221 removed outlier: 7.086A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.908A pdb=" N ILE G 137 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN G 192 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 471 through 473 removed outlier: 6.505A pdb=" N ILE G 472 " --> pdb=" O VAL G 698 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 604 " --> pdb=" O VAL G 599 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 232 through 238 removed outlier: 8.374A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 141 removed outlier: 4.902A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.093A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) 1887 hydrogen bonds defined for protein. 5508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11604 1.34 - 1.46: 6395 1.46 - 1.58: 17330 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 35533 Sorted by residual: bond pdb=" N PRO E 623 " pdb=" CD PRO E 623 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" C HIS E 622 " pdb=" N PRO E 623 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.19e-02 7.06e+03 1.79e+01 bond pdb=" CG ARG C 410 " pdb=" CD ARG C 410 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.16e+00 bond pdb=" CB ARG C 410 " pdb=" CG ARG C 410 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.57e+00 bond pdb=" CG ARG D 350 " pdb=" CD ARG D 350 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.85e+00 ... (remaining 35528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 47418 2.60 - 5.20: 587 5.20 - 7.80: 88 7.80 - 10.40: 19 10.40 - 13.00: 2 Bond angle restraints: 48114 Sorted by residual: angle pdb=" N ILE A 429 " pdb=" CA ILE A 429 " pdb=" C ILE A 429 " ideal model delta sigma weight residual 112.96 106.96 6.00 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N ILE D 429 " pdb=" CA ILE D 429 " pdb=" C ILE D 429 " ideal model delta sigma weight residual 112.96 106.99 5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.97 5.56 9.80e-01 1.04e+00 3.22e+01 angle pdb=" CA GLU D 397 " pdb=" CB GLU D 397 " pdb=" CG GLU D 397 " ideal model delta sigma weight residual 114.10 124.03 -9.93 2.00e+00 2.50e-01 2.47e+01 angle pdb=" CA GLU A 397 " pdb=" CB GLU A 397 " pdb=" CG GLU A 397 " ideal model delta sigma weight residual 114.10 123.98 -9.88 2.00e+00 2.50e-01 2.44e+01 ... (remaining 48109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 20471 17.71 - 35.42: 1147 35.42 - 53.13: 114 53.13 - 70.84: 37 70.84 - 88.55: 23 Dihedral angle restraints: 21792 sinusoidal: 8719 harmonic: 13073 Sorted by residual: dihedral pdb=" CA HIS C 576 " pdb=" C HIS C 576 " pdb=" N LYS C 577 " pdb=" CA LYS C 577 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLU D 113 " pdb=" C GLU D 113 " pdb=" N GLN D 114 " pdb=" CA GLN D 114 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N GLN A 114 " pdb=" CA GLN A 114 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 21789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4029 0.046 - 0.091: 1309 0.091 - 0.137: 380 0.137 - 0.182: 48 0.182 - 0.228: 7 Chirality restraints: 5773 Sorted by residual: chirality pdb=" CG LEU D 108 " pdb=" CB LEU D 108 " pdb=" CD1 LEU D 108 " pdb=" CD2 LEU D 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 108 " pdb=" CB LEU A 108 " pdb=" CD1 LEU A 108 " pdb=" CD2 LEU A 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 412 " pdb=" CA ILE B 412 " pdb=" CG1 ILE B 412 " pdb=" CG2 ILE B 412 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5770 not shown) Planarity restraints: 6156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 142 " -0.063 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO B 143 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 447 " 0.015 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" CG PHE E 447 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 447 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 447 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 447 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 447 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 394 " -0.087 9.50e-02 1.11e+02 4.37e-02 5.67e+00 pdb=" NE ARG D 394 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 394 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG D 394 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 394 " 0.010 2.00e-02 2.50e+03 ... (remaining 6153 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 718 2.67 - 3.22: 37164 3.22 - 3.78: 53498 3.78 - 4.34: 74948 4.34 - 4.90: 118404 Nonbonded interactions: 284732 Sorted by model distance: nonbonded pdb=" NH1 ARG F 139 " pdb=" O LEU F 140 " model vdw 2.108 3.120 nonbonded pdb=" NZ LYS A 197 " pdb=" O PRO A 198 " model vdw 2.199 3.120 nonbonded pdb=" NZ LYS D 197 " pdb=" O PRO D 198 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU B 89 " pdb=" OH TYR B 255 " model vdw 2.210 3.040 nonbonded pdb=" NH2 ARG C 410 " pdb=" O ASN D 399 " model vdw 2.211 3.120 ... (remaining 284727 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'C' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'E' and (resid 17 through 261 or resid 406 through 709)) selection = chain 'F' selection = (chain 'G' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'H' and (resid 17 through 261 or resid 406 through 709)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 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: 0.060 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 33.720 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 35533 Z= 0.307 Angle : 0.783 13.000 48114 Z= 0.436 Chirality : 0.048 0.228 5773 Planarity : 0.004 0.094 6156 Dihedral : 11.525 88.548 13354 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 4479 helix: -0.43 (0.11), residues: 2101 sheet: 0.08 (0.20), residues: 671 loop : -1.84 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG D 394 TYR 0.019 0.002 TYR E 658 PHE 0.042 0.002 PHE E 447 TRP 0.008 0.001 TRP E 477 HIS 0.008 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00683 (35533) covalent geometry : angle 0.78339 (48114) hydrogen bonds : bond 0.17419 ( 1887) hydrogen bonds : angle 7.05277 ( 5508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7906 (tpt) cc_final: 0.7666 (tpt) REVERT: A 255 TYR cc_start: 0.7945 (t80) cc_final: 0.7328 (t80) REVERT: D 128 MET cc_start: 0.7583 (tpt) cc_final: 0.6899 (tpp) REVERT: D 136 ASP cc_start: 0.8626 (t0) cc_final: 0.8279 (t0) REVERT: E 43 PHE cc_start: 0.8288 (m-80) cc_final: 0.8024 (m-10) REVERT: E 522 MET cc_start: 0.7588 (ptp) cc_final: 0.7227 (ptp) REVERT: G 97 MET cc_start: 0.8258 (tmm) cc_final: 0.8051 (tmm) REVERT: G 141 TYR cc_start: 0.8477 (t80) cc_final: 0.8113 (t80) REVERT: G 157 LEU cc_start: 0.9078 (tp) cc_final: 0.8822 (tp) REVERT: H 117 PHE cc_start: 0.7683 (p90) cc_final: 0.7286 (t80) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2201 time to fit residues: 150.5845 Evaluate side-chains 293 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 40.0000 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 114 GLN A 275 ASN A 340 HIS A 571 HIS A 589 GLN B 408 ASN C 259 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN E 192 ASN E 259 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078779 restraints weight = 80766.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082463 restraints weight = 43219.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083009 restraints weight = 27340.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083673 restraints weight = 23265.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084043 restraints weight = 22368.315| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35533 Z= 0.142 Angle : 0.626 11.326 48114 Z= 0.314 Chirality : 0.046 0.226 5773 Planarity : 0.004 0.077 6156 Dihedral : 4.397 24.832 4836 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.24 % Allowed : 6.78 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4479 helix: 0.35 (0.11), residues: 2174 sheet: 0.44 (0.21), residues: 640 loop : -1.59 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 385 TYR 0.020 0.001 TYR A 343 PHE 0.028 0.001 PHE C 273 TRP 0.005 0.001 TRP A 631 HIS 0.010 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00312 (35533) covalent geometry : angle 0.62602 (48114) hydrogen bonds : bond 0.04319 ( 1887) hydrogen bonds : angle 4.86564 ( 5508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 365 time to evaluate : 1.298 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: A 128 MET cc_start: 0.7837 (tpt) cc_final: 0.7627 (tpp) REVERT: B 234 LEU cc_start: 0.9234 (mt) cc_final: 0.9027 (mp) REVERT: B 462 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 428 ILE cc_start: 0.8652 (mm) cc_final: 0.8347 (mm) REVERT: D 128 MET cc_start: 0.7598 (tpt) cc_final: 0.6984 (tpp) REVERT: D 136 ASP cc_start: 0.8672 (t0) cc_final: 0.8459 (t0) REVERT: E 43 PHE cc_start: 0.8360 (m-80) cc_final: 0.8073 (m-80) REVERT: E 259 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8503 (t0) REVERT: E 522 MET cc_start: 0.7728 (ptp) cc_final: 0.7314 (ptp) REVERT: E 540 MET cc_start: 0.8651 (tmm) cc_final: 0.8175 (tmm) REVERT: F 26 LEU cc_start: 0.9534 (mt) cc_final: 0.9292 (pp) REVERT: F 42 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9111 (tt) REVERT: F 43 PHE cc_start: 0.8739 (m-80) cc_final: 0.8469 (m-80) REVERT: G 97 MET cc_start: 0.8293 (tmm) cc_final: 0.8037 (tmm) REVERT: G 141 TYR cc_start: 0.8537 (t80) cc_final: 0.8219 (t80) REVERT: H 117 PHE cc_start: 0.7553 (p90) cc_final: 0.7266 (t80) REVERT: H 432 ILE cc_start: 0.8208 (mm) cc_final: 0.7988 (tp) outliers start: 48 outliers final: 29 residues processed: 381 average time/residue: 0.2015 time to fit residues: 125.9291 Evaluate side-chains 339 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 447 PHE Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 289 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 366 optimal weight: 30.0000 chunk 299 optimal weight: 5.9990 chunk 437 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 175 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 571 HIS C 192 ASN C 576 HIS D 62 GLN D 114 GLN D 340 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 ASN H 546 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.122198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.078120 restraints weight = 80840.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081927 restraints weight = 44131.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082290 restraints weight = 27383.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082827 restraints weight = 23805.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083152 restraints weight = 23699.200| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35533 Z= 0.158 Angle : 0.608 12.913 48114 Z= 0.302 Chirality : 0.045 0.206 5773 Planarity : 0.004 0.047 6156 Dihedral : 4.232 23.933 4836 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.73 % Allowed : 9.21 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4479 helix: 0.69 (0.11), residues: 2171 sheet: 0.36 (0.21), residues: 682 loop : -1.41 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.014 0.001 TYR E 569 PHE 0.027 0.001 PHE C 273 TRP 0.008 0.001 TRP A 631 HIS 0.011 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00357 (35533) covalent geometry : angle 0.60789 (48114) hydrogen bonds : bond 0.04076 ( 1887) hydrogen bonds : angle 4.62950 ( 5508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 1.363 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: A 108 LEU cc_start: 0.9353 (mt) cc_final: 0.9115 (mt) REVERT: B 462 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: C 428 ILE cc_start: 0.8657 (mm) cc_final: 0.8324 (mm) REVERT: D 128 MET cc_start: 0.7670 (tpt) cc_final: 0.7101 (tpp) REVERT: E 43 PHE cc_start: 0.8382 (m-80) cc_final: 0.8100 (m-80) REVERT: E 540 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: F 42 LEU cc_start: 0.9352 (mm) cc_final: 0.9073 (tt) REVERT: F 43 PHE cc_start: 0.8720 (m-80) cc_final: 0.8362 (m-80) REVERT: F 540 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (ttp) REVERT: G 97 MET cc_start: 0.8380 (tmm) cc_final: 0.8114 (tmm) REVERT: G 136 ASP cc_start: 0.8751 (t0) cc_final: 0.8535 (t0) REVERT: G 141 TYR cc_start: 0.8530 (t80) cc_final: 0.8311 (t80) REVERT: H 117 PHE cc_start: 0.7541 (p90) cc_final: 0.7217 (t80) outliers start: 67 outliers final: 32 residues processed: 363 average time/residue: 0.2118 time to fit residues: 126.9668 Evaluate side-chains 337 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 540 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 200 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 134 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 396 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 571 HIS B 114 GLN E 192 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN H 420 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.077941 restraints weight = 80759.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081316 restraints weight = 43935.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082338 restraints weight = 26791.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082741 restraints weight = 23879.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082971 restraints weight = 22765.055| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35533 Z= 0.170 Angle : 0.611 11.761 48114 Z= 0.302 Chirality : 0.045 0.209 5773 Planarity : 0.004 0.044 6156 Dihedral : 4.210 23.349 4836 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.73 % Allowed : 10.63 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4479 helix: 0.86 (0.11), residues: 2165 sheet: 0.39 (0.21), residues: 680 loop : -1.31 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.012 0.001 TYR E 569 PHE 0.040 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.012 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00386 (35533) covalent geometry : angle 0.61074 (48114) hydrogen bonds : bond 0.03874 ( 1887) hydrogen bonds : angle 4.53600 ( 5508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8977 (mt) cc_final: 0.8753 (pp) REVERT: B 453 ARG cc_start: 0.7623 (mmp80) cc_final: 0.7376 (mmp-170) REVERT: B 462 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: C 428 ILE cc_start: 0.8683 (mm) cc_final: 0.8294 (mm) REVERT: D 109 GLN cc_start: 0.8802 (pm20) cc_final: 0.8485 (pm20) REVERT: D 128 MET cc_start: 0.7674 (tpt) cc_final: 0.7091 (tpp) REVERT: D 343 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7975 (t80) REVERT: E 43 PHE cc_start: 0.8423 (m-80) cc_final: 0.8118 (m-80) REVERT: F 42 LEU cc_start: 0.9372 (mm) cc_final: 0.9080 (tt) REVERT: F 43 PHE cc_start: 0.8782 (m-80) cc_final: 0.8365 (m-80) REVERT: G 97 MET cc_start: 0.8394 (tmm) cc_final: 0.8098 (tmm) REVERT: G 141 TYR cc_start: 0.8631 (t80) cc_final: 0.8403 (t80) REVERT: G 642 ASP cc_start: 0.7502 (t0) cc_final: 0.7284 (t0) REVERT: H 49 LEU cc_start: 0.9340 (tp) cc_final: 0.9062 (tt) REVERT: H 117 PHE cc_start: 0.7425 (p90) cc_final: 0.7191 (t80) outliers start: 67 outliers final: 47 residues processed: 359 average time/residue: 0.2131 time to fit residues: 125.9912 Evaluate side-chains 339 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 343 TYR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 90 optimal weight: 30.0000 chunk 414 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 402 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 300 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 396 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN C 114 GLN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078597 restraints weight = 80327.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.081378 restraints weight = 41451.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083334 restraints weight = 28634.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084499 restraints weight = 23177.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084936 restraints weight = 20506.388| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35533 Z= 0.117 Angle : 0.587 13.010 48114 Z= 0.285 Chirality : 0.044 0.291 5773 Planarity : 0.003 0.042 6156 Dihedral : 4.003 22.111 4836 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.42 % Allowed : 11.80 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4479 helix: 1.00 (0.11), residues: 2180 sheet: 0.44 (0.21), residues: 690 loop : -1.21 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 452 TYR 0.011 0.001 TYR D 388 PHE 0.043 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.011 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00256 (35533) covalent geometry : angle 0.58680 (48114) hydrogen bonds : bond 0.03574 ( 1887) hydrogen bonds : angle 4.33426 ( 5508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 1.379 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: B 462 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 428 ILE cc_start: 0.8688 (mm) cc_final: 0.8291 (mm) REVERT: D 109 GLN cc_start: 0.8762 (pm20) cc_final: 0.8490 (pm20) REVERT: D 128 MET cc_start: 0.7446 (tpt) cc_final: 0.6922 (tpp) REVERT: D 343 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7620 (t80) REVERT: E 128 MET cc_start: 0.7695 (tpt) cc_final: 0.7316 (tpt) REVERT: E 450 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7580 (t80) REVERT: F 42 LEU cc_start: 0.9388 (mm) cc_final: 0.9085 (tt) REVERT: F 43 PHE cc_start: 0.8797 (m-80) cc_final: 0.8389 (m-80) REVERT: G 97 MET cc_start: 0.8349 (tmm) cc_final: 0.8028 (tmm) REVERT: G 141 TYR cc_start: 0.8432 (t80) cc_final: 0.8171 (t80) REVERT: G 190 LEU cc_start: 0.8649 (mm) cc_final: 0.8256 (mm) REVERT: H 49 LEU cc_start: 0.9276 (tp) cc_final: 0.8985 (tt) outliers start: 55 outliers final: 36 residues processed: 357 average time/residue: 0.2148 time to fit residues: 125.8839 Evaluate side-chains 335 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 343 TYR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 447 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 28 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 374 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 HIS G 576 HIS H 246 HIS H 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076133 restraints weight = 80029.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078582 restraints weight = 42797.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080245 restraints weight = 30226.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081180 restraints weight = 24699.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081869 restraints weight = 22021.368| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 35533 Z= 0.283 Angle : 0.694 13.690 48114 Z= 0.343 Chirality : 0.047 0.352 5773 Planarity : 0.004 0.038 6156 Dihedral : 4.429 22.576 4836 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.84 % Allowed : 12.78 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4479 helix: 0.83 (0.11), residues: 2181 sheet: 0.33 (0.20), residues: 723 loop : -1.30 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 126 TYR 0.023 0.002 TYR F 569 PHE 0.043 0.002 PHE B 43 TRP 0.007 0.001 TRP A 631 HIS 0.009 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00659 (35533) covalent geometry : angle 0.69426 (48114) hydrogen bonds : bond 0.04125 ( 1887) hydrogen bonds : angle 4.66533 ( 5508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 1.421 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: B 42 LEU cc_start: 0.8970 (mt) cc_final: 0.8755 (pp) REVERT: B 462 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: C 92 LEU cc_start: 0.8838 (tt) cc_final: 0.8585 (tt) REVERT: C 227 LYS cc_start: 0.8692 (tppt) cc_final: 0.8492 (tppt) REVERT: C 428 ILE cc_start: 0.8715 (mm) cc_final: 0.8311 (mm) REVERT: D 128 MET cc_start: 0.7445 (tpt) cc_final: 0.6965 (tpp) REVERT: E 128 MET cc_start: 0.7766 (tpt) cc_final: 0.7046 (tpp) REVERT: E 450 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (t80) REVERT: F 42 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9047 (tt) REVERT: F 43 PHE cc_start: 0.8701 (m-80) cc_final: 0.8299 (m-80) REVERT: G 97 MET cc_start: 0.8325 (tmm) cc_final: 0.8079 (tmm) REVERT: G 190 LEU cc_start: 0.8682 (mm) cc_final: 0.8290 (mm) REVERT: H 49 LEU cc_start: 0.9157 (tp) cc_final: 0.8890 (tt) REVERT: H 540 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7788 (ttm) outliers start: 71 outliers final: 52 residues processed: 333 average time/residue: 0.2147 time to fit residues: 119.3075 Evaluate side-chains 338 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 521 MET Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 540 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 330 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 376 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 439 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 443 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 23 optimal weight: 40.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 ASN E 114 GLN E 259 ASN H 246 HIS H 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.121729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079119 restraints weight = 79633.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081691 restraints weight = 41587.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083557 restraints weight = 29029.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084621 restraints weight = 23422.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085262 restraints weight = 20732.569| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35533 Z= 0.125 Angle : 0.618 13.019 48114 Z= 0.296 Chirality : 0.045 0.332 5773 Planarity : 0.003 0.039 6156 Dihedral : 4.051 24.621 4836 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.66 % Allowed : 13.69 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4479 helix: 1.05 (0.11), residues: 2190 sheet: 0.24 (0.20), residues: 702 loop : -1.21 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 139 TYR 0.024 0.001 TYR G 141 PHE 0.044 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00278 (35533) covalent geometry : angle 0.61796 (48114) hydrogen bonds : bond 0.03581 ( 1887) hydrogen bonds : angle 4.36060 ( 5508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 1.353 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: A 453 ARG cc_start: 0.7342 (mmp80) cc_final: 0.7138 (mmp-170) REVERT: B 462 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 428 ILE cc_start: 0.8658 (mm) cc_final: 0.8284 (mm) REVERT: D 128 MET cc_start: 0.7432 (tpt) cc_final: 0.6934 (tpp) REVERT: D 343 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7497 (t80) REVERT: E 128 MET cc_start: 0.7795 (tpt) cc_final: 0.7066 (tpp) REVERT: E 259 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8660 (t0) REVERT: E 450 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7587 (t80) REVERT: F 42 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9088 (tt) REVERT: F 43 PHE cc_start: 0.8739 (m-80) cc_final: 0.8315 (m-80) REVERT: G 97 MET cc_start: 0.8367 (tmm) cc_final: 0.8081 (tmm) REVERT: G 190 LEU cc_start: 0.8673 (mm) cc_final: 0.8250 (mm) REVERT: G 642 ASP cc_start: 0.7440 (t0) cc_final: 0.7206 (t0) REVERT: H 141 TYR cc_start: 0.8455 (t80) cc_final: 0.8149 (t80) outliers start: 64 outliers final: 44 residues processed: 337 average time/residue: 0.2060 time to fit residues: 116.1534 Evaluate side-chains 336 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 343 TYR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 447 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 333 optimal weight: 0.8980 chunk 432 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 411 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 425 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN E 259 ASN H 246 HIS H 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.120117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.077710 restraints weight = 80068.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081204 restraints weight = 43600.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082119 restraints weight = 26410.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082415 restraints weight = 22468.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082837 restraints weight = 22511.738| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 35533 Z= 0.196 Angle : 0.670 16.422 48114 Z= 0.322 Chirality : 0.046 0.366 5773 Planarity : 0.003 0.039 6156 Dihedral : 4.182 25.939 4836 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.50 % Allowed : 14.39 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4479 helix: 0.99 (0.11), residues: 2190 sheet: 0.23 (0.20), residues: 718 loop : -1.19 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 394 TYR 0.022 0.001 TYR F 569 PHE 0.055 0.002 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00454 (35533) covalent geometry : angle 0.67045 (48114) hydrogen bonds : bond 0.03800 ( 1887) hydrogen bonds : angle 4.48400 ( 5508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 1.345 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: A 42 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8855 (pp) REVERT: A 110 ILE cc_start: 0.9387 (mp) cc_final: 0.9166 (pt) REVERT: B 462 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: C 410 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7580 (ttm170) REVERT: C 428 ILE cc_start: 0.8668 (mm) cc_final: 0.8289 (mm) REVERT: D 128 MET cc_start: 0.7581 (tpt) cc_final: 0.7061 (tpp) REVERT: D 343 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.7490 (t80) REVERT: E 128 MET cc_start: 0.7961 (tpt) cc_final: 0.7268 (tpp) REVERT: E 259 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8617 (t0) REVERT: E 450 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7676 (t80) REVERT: F 42 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9070 (tt) REVERT: F 43 PHE cc_start: 0.8794 (m-80) cc_final: 0.8333 (m-80) REVERT: G 190 LEU cc_start: 0.8771 (mm) cc_final: 0.8384 (mm) REVERT: H 141 TYR cc_start: 0.8649 (t80) cc_final: 0.8310 (t80) outliers start: 58 outliers final: 49 residues processed: 318 average time/residue: 0.1980 time to fit residues: 105.7595 Evaluate side-chains 345 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 343 TYR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 54 optimal weight: 3.9990 chunk 357 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 367 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 406 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 259 ASN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN H 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078562 restraints weight = 80348.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081180 restraints weight = 42011.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082984 restraints weight = 29367.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083940 restraints weight = 23912.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084725 restraints weight = 21337.894| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35533 Z= 0.131 Angle : 0.643 16.611 48114 Z= 0.304 Chirality : 0.045 0.379 5773 Planarity : 0.003 0.040 6156 Dihedral : 3.989 25.962 4836 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.32 % Allowed : 14.75 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4479 helix: 1.11 (0.11), residues: 2194 sheet: 0.17 (0.20), residues: 721 loop : -1.11 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 394 TYR 0.018 0.001 TYR F 569 PHE 0.058 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00295 (35533) covalent geometry : angle 0.64265 (48114) hydrogen bonds : bond 0.03525 ( 1887) hydrogen bonds : angle 4.33300 ( 5508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 1.340 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: A 42 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 462 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: C 428 ILE cc_start: 0.8608 (mm) cc_final: 0.8235 (mm) REVERT: D 109 GLN cc_start: 0.8804 (pm20) cc_final: 0.8519 (pt0) REVERT: D 128 MET cc_start: 0.7473 (tpt) cc_final: 0.6999 (tpp) REVERT: E 128 MET cc_start: 0.7818 (tpt) cc_final: 0.7141 (tpp) REVERT: E 259 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8793 (t0) REVERT: E 450 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7616 (t80) REVERT: F 42 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9085 (tt) REVERT: F 43 PHE cc_start: 0.8771 (m-80) cc_final: 0.8334 (m-80) REVERT: G 139 ARG cc_start: 0.7605 (tpt90) cc_final: 0.7399 (tpt90) REVERT: G 190 LEU cc_start: 0.8633 (mm) cc_final: 0.8159 (mm) REVERT: H 141 TYR cc_start: 0.8532 (t80) cc_final: 0.8249 (t80) outliers start: 51 outliers final: 44 residues processed: 329 average time/residue: 0.2055 time to fit residues: 112.6071 Evaluate side-chains 341 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 449 optimal weight: 0.8980 chunk 426 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 402 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 0.0070 chunk 235 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 259 ASN H 246 HIS H 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081056 restraints weight = 80474.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083930 restraints weight = 41290.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085877 restraints weight = 28346.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086768 restraints weight = 22867.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087683 restraints weight = 20420.618| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35533 Z= 0.104 Angle : 0.632 17.405 48114 Z= 0.297 Chirality : 0.045 0.409 5773 Planarity : 0.003 0.043 6156 Dihedral : 3.775 26.154 4836 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.11 % Allowed : 15.03 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4479 helix: 1.28 (0.11), residues: 2189 sheet: 0.22 (0.21), residues: 705 loop : -1.02 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 394 TYR 0.028 0.001 TYR D 343 PHE 0.062 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00224 (35533) covalent geometry : angle 0.63197 (48114) hydrogen bonds : bond 0.03307 ( 1887) hydrogen bonds : angle 4.19151 ( 5508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 323 time to evaluate : 1.399 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: A 42 LEU cc_start: 0.9134 (mm) cc_final: 0.8868 (pp) REVERT: A 438 LEU cc_start: 0.7945 (mm) cc_final: 0.7644 (tt) REVERT: C 428 ILE cc_start: 0.8509 (mm) cc_final: 0.8142 (mm) REVERT: D 128 MET cc_start: 0.7431 (tpt) cc_final: 0.6954 (tpp) REVERT: E 128 MET cc_start: 0.7777 (tpt) cc_final: 0.7132 (tpp) REVERT: E 450 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7642 (t80) REVERT: E 459 GLU cc_start: 0.7562 (mp0) cc_final: 0.7339 (mp0) REVERT: F 42 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9094 (tt) REVERT: F 43 PHE cc_start: 0.8772 (m-80) cc_final: 0.8303 (m-80) REVERT: G 97 MET cc_start: 0.8092 (tmm) cc_final: 0.7808 (tmm) REVERT: G 190 LEU cc_start: 0.8608 (mm) cc_final: 0.8173 (mm) outliers start: 43 outliers final: 35 residues processed: 345 average time/residue: 0.2018 time to fit residues: 116.1590 Evaluate side-chains 337 residues out of total 3865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 343 TYR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 658 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 PHE Chi-restraints excluded: chain G residue 540 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 159 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 233 optimal weight: 0.0670 chunk 414 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 358 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 402 optimal weight: 0.9980 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS H 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079391 restraints weight = 79330.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081952 restraints weight = 41710.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083708 restraints weight = 28995.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084813 restraints weight = 23577.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085245 restraints weight = 20844.337| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35533 Z= 0.146 Angle : 0.655 17.140 48114 Z= 0.309 Chirality : 0.046 0.395 5773 Planarity : 0.003 0.040 6156 Dihedral : 3.898 26.540 4836 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.14 % Allowed : 14.93 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4479 helix: 1.27 (0.11), residues: 2190 sheet: 0.16 (0.20), residues: 748 loop : -0.97 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 394 TYR 0.017 0.001 TYR A 569 PHE 0.062 0.001 PHE B 43 TRP 0.008 0.001 TRP A 631 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00334 (35533) covalent geometry : angle 0.65478 (48114) hydrogen bonds : bond 0.03496 ( 1887) hydrogen bonds : angle 4.27936 ( 5508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6982.24 seconds wall clock time: 120 minutes 57.94 seconds (7257.94 seconds total)