Starting phenix.real_space_refine on Wed Aug 27 01:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mdp_9103/08_2025/6mdp_9103.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 124 5.16 5 C 14117 2.51 5 N 3901 2.21 5 O 4260 1.98 5 H 22777 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45210 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8088 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 8167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 8167 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 23, 'TRANS': 492} Chain breaks: 1 Chain: "C" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8337 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 23, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8314 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 23, 'TRANS': 502} Chain breaks: 1 Chain: "E" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7788 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 20, 'TRANS': 471} Chain breaks: 2 Chain: "F" Number of atoms: 3906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3906 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 277 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.61, per 1000 atoms: 0.15 Number of scatterers: 45210 At special positions: 0 Unit cell: (144.1, 141.48, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 31 15.00 O 4260 8.00 N 3901 7.00 C 14117 6.00 H 22777 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 14 sheets defined 51.7% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.981A pdb=" N ASP A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.994A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.656A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.685A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.842A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 removed outlier: 3.609A pdb=" N SER A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 399 through 418 removed outlier: 4.210A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 4.125A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 455 Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.729A pdb=" N SER A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.688A pdb=" N ALA A 500 " --> pdb=" O GLN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 530 removed outlier: 4.201A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.493A pdb=" N ALA A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.768A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 589 " --> pdb=" O MET A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 619 through 632 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.977A pdb=" N GLN A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.991A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.570A pdb=" N LYS A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 removed outlier: 4.002A pdb=" N ARG B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.649A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.728A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 removed outlier: 4.262A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 399 through 416 removed outlier: 3.922A pdb=" N THR B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.633A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.554A pdb=" N ILE B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.682A pdb=" N ASP B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 530 removed outlier: 4.272A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.671A pdb=" N ASN B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 4.440A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 589 " --> pdb=" O MET B 585 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 595 " --> pdb=" O ASP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 619 through 631 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 656 through 661 removed outlier: 4.075A pdb=" N ALA B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.891A pdb=" N GLU B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.681A pdb=" N THR B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 719 removed outlier: 4.122A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'C' and resid 223 through 235 removed outlier: 3.907A pdb=" N ILE C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.628A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 273 removed outlier: 3.595A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 296 through 307 removed outlier: 4.020A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 346 through 360 removed outlier: 3.934A pdb=" N VAL C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.772A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 417 removed outlier: 3.758A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 431 removed outlier: 4.056A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 458 removed outlier: 4.230A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 457 " --> pdb=" O MET C 453 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 511 through 530 removed outlier: 4.046A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 527 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.704A pdb=" N LEU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 619 through 631 removed outlier: 3.529A pdb=" N LEU C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 655 Processing helix chain 'C' and resid 673 through 684 removed outlier: 3.902A pdb=" N GLU C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 700 removed outlier: 3.845A pdb=" N GLN C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN C 697 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 719 removed outlier: 3.711A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 737 removed outlier: 4.396A pdb=" N VAL C 726 " --> pdb=" O PRO C 722 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 235 Processing helix chain 'D' and resid 241 through 249 Processing helix chain 'D' and resid 265 through 277 removed outlier: 4.351A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 315 removed outlier: 4.722A pdb=" N ILE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 removed outlier: 4.038A pdb=" N ILE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 360 Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'D' and resid 399 through 417 removed outlier: 4.451A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 438 through 458 removed outlier: 3.998A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 removed outlier: 3.689A pdb=" N SER D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 4.494A pdb=" N VAL D 514 " --> pdb=" O TRP D 510 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 4.007A pdb=" N ILE D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.805A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 632 removed outlier: 3.681A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 655 Processing helix chain 'D' and resid 672 through 682 removed outlier: 4.458A pdb=" N GLU D 678 " --> pdb=" O GLU D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 702 removed outlier: 4.034A pdb=" N GLN D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 700 " --> pdb=" O GLN D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 719 removed outlier: 3.824A pdb=" N GLU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 734 removed outlier: 3.817A pdb=" N ALA D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 removed outlier: 4.146A pdb=" N PHE E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 277 removed outlier: 3.911A pdb=" N ALA E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.594A pdb=" N ILE E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 removed outlier: 3.597A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA E 307 " --> pdb=" O ARG E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 351 through 360 removed outlier: 4.250A pdb=" N ILE E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 384 removed outlier: 4.400A pdb=" N ILE E 379 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU E 381 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 417 removed outlier: 3.931A pdb=" N GLN E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 409 " --> pdb=" O GLN E 405 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 431 Processing helix chain 'E' and resid 439 through 441 No H-bonds generated for 'chain 'E' and resid 439 through 441' Processing helix chain 'E' and resid 442 through 454 removed outlier: 3.656A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 489 removed outlier: 4.015A pdb=" N GLU E 485 " --> pdb=" O LEU E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 530 removed outlier: 3.776A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 560 removed outlier: 3.856A pdb=" N SER E 560 " --> pdb=" O ILE E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 595 removed outlier: 3.735A pdb=" N CYS E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 619 through 632 removed outlier: 3.600A pdb=" N VAL E 628 " --> pdb=" O GLN E 624 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 655 Processing helix chain 'E' and resid 656 through 661 removed outlier: 3.891A pdb=" N ALA E 660 " --> pdb=" O GLU E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 684 Processing helix chain 'E' and resid 687 through 696 removed outlier: 3.703A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 720 removed outlier: 4.231A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET E 716 " --> pdb=" O MET E 712 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER E 717 " --> pdb=" O LEU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 736 removed outlier: 4.710A pdb=" N VAL E 726 " --> pdb=" O PRO E 722 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG E 727 " --> pdb=" O GLU E 723 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS E 728 " --> pdb=" O TYR E 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 530 removed outlier: 4.291A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 561 Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.941A pdb=" N PHE F 589 " --> pdb=" O MET F 585 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER F 595 " --> pdb=" O ASP F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 610 Processing helix chain 'F' and resid 619 through 632 removed outlier: 3.542A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 655 Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 700 removed outlier: 4.112A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY F 700 " --> pdb=" O GLN F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 718 removed outlier: 3.750A pdb=" N MET F 712 " --> pdb=" O LYS F 708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 725 removed outlier: 4.231A pdb=" N TYR F 724 " --> pdb=" O MET F 720 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG F 725 " --> pdb=" O ASP F 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 720 through 725' Processing helix chain 'F' and resid 725 through 738 removed outlier: 3.890A pdb=" N GLU F 735 " --> pdb=" O ALA F 731 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU F 736 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 286 removed outlier: 6.912A pdb=" N GLU A 281 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE A 326 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 283 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP A 328 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 285 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 540 removed outlier: 6.157A pdb=" N VAL A 539 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ASP A 603 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS A 568 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 285 through 286 removed outlier: 4.546A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 566 through 567 removed outlier: 6.805A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 646 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 672 removed outlier: 3.971A pdb=" N ALA B 671 " --> pdb=" O VAL B 703 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 259 removed outlier: 3.561A pdb=" N LEU C 368 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 326 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 565 through 568 removed outlier: 6.882A pdb=" N LYS C 566 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 537 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY C 644 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 539 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N THR C 663 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER C 538 " --> pdb=" O THR C 663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 670 through 672 removed outlier: 5.715A pdb=" N VAL C 703 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 256 through 258 removed outlier: 3.988A pdb=" N MET D 393 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 324 through 325 Processing sheet with id=AB2, first strand: chain 'D' and resid 564 through 568 removed outlier: 4.137A pdb=" N THR D 646 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 540 " --> pdb=" O THR D 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 257 through 259 Processing sheet with id=AB4, first strand: chain 'E' and resid 564 through 568 removed outlier: 3.994A pdb=" N PHE E 564 " --> pdb=" O LEU E 597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS E 566 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR E 646 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 537 through 540 removed outlier: 6.471A pdb=" N VAL F 537 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLY F 644 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL F 539 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 564 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL F 601 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASP F 603 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS F 568 " --> pdb=" O ASP F 603 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2649 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: 9.34 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22745 1.03 - 1.22: 49 1.22 - 1.42: 8815 1.42 - 1.62: 13733 1.62 - 1.82: 216 Bond restraints: 45558 Sorted by residual: bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C4 ATP D 802 " pdb=" C5 ATP D 802 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP B 802 " pdb=" C5 ATP B 802 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 ... (remaining 45553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.51: 82579 6.51 - 13.02: 182 13.02 - 19.53: 15 19.53 - 26.03: 93 26.03 - 32.54: 14 Bond angle restraints: 82883 Sorted by residual: angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 115.29 24.58 1.00e+00 1.00e+00 6.04e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 116.11 23.76 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PA ATP F 801 " pdb=" O3A ATP F 801 " pdb=" PB ATP F 801 " ideal model delta sigma weight residual 136.83 114.54 22.29 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 117.62 22.25 1.00e+00 1.00e+00 4.95e+02 ... (remaining 82878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 20508 32.46 - 64.93: 612 64.93 - 97.39: 44 97.39 - 129.86: 2 129.86 - 162.32: 2 Dihedral angle restraints: 21168 sinusoidal: 12241 harmonic: 8927 Sorted by residual: dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 102.33 -162.32 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O2A ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PA ADP E 802 " pdb=" PB ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 84.48 -144.48 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PB ADP E 802 " pdb=" PA ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 56.55 -116.55 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 21165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.417: 3490 0.417 - 0.835: 0 0.835 - 1.252: 0 1.252 - 1.669: 11 1.669 - 2.087: 17 Chirality restraints: 3518 Sorted by residual: chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -0.50 -2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" CG LEU A 419 " pdb=" CB LEU A 419 " pdb=" CD1 LEU A 419 " pdb=" CD2 LEU A 419 " both_signs ideal model delta sigma weight residual False -2.59 -0.51 -2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" CG LEU E 384 " pdb=" CB LEU E 384 " pdb=" CD1 LEU E 384 " pdb=" CD2 LEU E 384 " both_signs ideal model delta sigma weight residual False -2.59 -0.58 -2.01 2.00e-01 2.50e+01 1.01e+02 ... (remaining 3515 not shown) Planarity restraints: 6616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " 0.045 2.00e-02 2.50e+03 6.49e-02 6.31e+01 pdb=" CG ASN B 486 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " -0.110 2.00e-02 2.50e+03 pdb="HD21 ASN B 486 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 486 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 278 " -0.040 2.00e-02 2.50e+03 5.65e-02 4.79e+01 pdb=" CG ASN D 278 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN D 278 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 278 " 0.092 2.00e-02 2.50e+03 pdb="HD21 ASN D 278 " 0.013 2.00e-02 2.50e+03 pdb="HD22 ASN D 278 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 418 " -0.046 2.00e-02 2.50e+03 5.52e-02 4.57e+01 pdb=" CD GLN D 418 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN D 418 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN D 418 " 0.084 2.00e-02 2.50e+03 pdb="HE21 GLN D 418 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 418 " -0.084 2.00e-02 2.50e+03 ... (remaining 6613 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 4235 2.23 - 2.82: 100561 2.82 - 3.41: 116124 3.41 - 4.01: 152664 4.01 - 4.60: 238375 Nonbonded interactions: 611959 Sorted by model distance: nonbonded pdb=" O SER A 531 " pdb=" HZ2 LYS A 639 " model vdw 1.633 2.450 nonbonded pdb=" HE2 LYS D 702 " pdb=" HZ3 LYS D 702 " model vdw 1.636 1.816 nonbonded pdb=" OD2 ASP E 331 " pdb="HH11 ARG E 375 " model vdw 1.642 2.450 nonbonded pdb=" O THR D 692 " pdb="HE22 GLN D 696 " model vdw 1.672 2.450 nonbonded pdb=" O PRO B 211 " pdb=" H ASN B 278 " model vdw 1.672 2.450 ... (remaining 611954 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' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 384 or (resid 385 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or \ resid 386 through 457 or resid 476 through 606 or (resid 607 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or r \ esid 608 through 738)) selection = (chain 'B' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 384 or (resid 385 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or \ resid 386 through 457 or resid 476 through 606 or (resid 607 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or r \ esid 608 through 738)) selection = (chain 'C' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 384 or (resid 385 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE or name HH11 or name HH12 or name HH22)) or resid 386 through 457 or \ resid 476 through 738)) selection = (chain 'D' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 457 or resid 476 through 606 or (resid 607 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name H \ B3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or na \ me HH12)) or resid 608 through 738)) selection = (chain 'E' and (resid 216 through 344 or (resid 345 and (name N or name CA or na \ me C or name O or name H or name HA2)) or resid 346 through 384 or (resid 385 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or \ name HH12 or name HH22)) or resid 386 through 457 or resid 476 through 606 or (r \ esid 607 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 608 through 738)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.820 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 35.770 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 : 0.010 0.848 22782 Z= 0.720 Angle : 1.424 26.166 30766 Z= 0.882 Chirality : 0.167 2.087 3518 Planarity : 0.007 0.072 3921 Dihedral : 13.116 162.323 9003 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 0.33 % Allowed : 7.28 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.13), residues: 2806 helix: -2.28 (0.12), residues: 1258 sheet: -2.40 (0.25), residues: 305 loop : -2.32 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 388 TYR 0.027 0.003 TYR A 502 PHE 0.043 0.004 PHE D 231 TRP 0.017 0.003 TRP D 704 HIS 0.043 0.003 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00887 (22781) covalent geometry : angle 1.42354 (30766) hydrogen bonds : bond 0.10719 ( 900) hydrogen bonds : angle 6.33870 ( 2649) Misc. bond : bond 0.84773 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.780 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.5494 (pp-130) cc_final: 0.4176 (pp-130) REVERT: C 340 MET cc_start: 0.1768 (mtm) cc_final: 0.0910 (mmt) REVERT: C 573 MET cc_start: 0.4995 (ptp) cc_final: 0.4638 (ptt) outliers start: 8 outliers final: 2 residues processed: 203 average time/residue: 0.3591 time to fit residues: 108.2722 Evaluate side-chains 138 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 566 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 353 GLN A 365 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN B 214 ASN B 352 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 319 ASN C 583 GLN C 620 ASN D 247 GLN D 278 ASN D 301 ASN D 374 ASN D 561 ASN D 675 GLN E 278 ASN E 474 GLN E 486 ASN E 620 ASN E 675 GLN F 527 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.027908 restraints weight = 585013.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.029293 restraints weight = 300555.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.030304 restraints weight = 186610.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.031022 restraints weight = 128658.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.031543 restraints weight = 96014.044| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22782 Z= 0.151 Angle : 0.832 27.427 30766 Z= 0.405 Chirality : 0.150 1.797 3518 Planarity : 0.005 0.066 3921 Dihedral : 11.589 160.202 3345 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 0.83 % Allowed : 9.96 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.14), residues: 2806 helix: -1.22 (0.13), residues: 1298 sheet: -1.98 (0.26), residues: 312 loop : -2.13 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 385 TYR 0.014 0.001 TYR A 502 PHE 0.017 0.001 PHE D 231 TRP 0.008 0.001 TRP D 213 HIS 0.008 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00338 (22781) covalent geometry : angle 0.83170 (30766) hydrogen bonds : bond 0.04782 ( 900) hydrogen bonds : angle 5.60234 ( 2649) Misc. bond : bond 0.00333 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.093 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9547 (mtp) cc_final: 0.9254 (ptp) REVERT: A 258 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 585 MET cc_start: 0.8653 (tmm) cc_final: 0.8224 (ppp) REVERT: A 657 MET cc_start: 0.9494 (tpp) cc_final: 0.9219 (tpp) REVERT: A 724 TYR cc_start: 0.8914 (m-80) cc_final: 0.8672 (m-80) REVERT: B 248 MET cc_start: 0.9549 (ttm) cc_final: 0.9232 (ttp) REVERT: B 552 LEU cc_start: 0.9883 (OUTLIER) cc_final: 0.9671 (mt) REVERT: B 573 MET cc_start: 0.8954 (ptp) cc_final: 0.8676 (ptp) REVERT: B 585 MET cc_start: 0.9858 (ttp) cc_final: 0.9631 (ttm) REVERT: C 340 MET cc_start: 0.1836 (mtm) cc_final: 0.1465 (mmt) REVERT: C 573 MET cc_start: 0.9000 (ptp) cc_final: 0.8669 (ptt) REVERT: C 712 MET cc_start: 0.8586 (tmm) cc_final: 0.8263 (tmm) REVERT: C 716 MET cc_start: 0.9316 (mtp) cc_final: 0.9097 (mmm) REVERT: E 499 TYR cc_start: 0.7595 (p90) cc_final: 0.7368 (p90) REVERT: E 716 MET cc_start: 0.9499 (ptp) cc_final: 0.9288 (ptp) REVERT: F 504 MET cc_start: 0.9153 (pmm) cc_final: 0.8877 (pmm) REVERT: F 712 MET cc_start: 0.9667 (tmt) cc_final: 0.9456 (tmm) REVERT: H 12 GLU cc_start: 0.8160 (pm20) cc_final: 0.7871 (pm20) outliers start: 20 outliers final: 10 residues processed: 159 average time/residue: 0.3286 time to fit residues: 81.1865 Evaluate side-chains 141 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 154 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 527 GLN A 583 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 620 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.032613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025108 restraints weight = 627944.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.026434 restraints weight = 321652.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.027400 restraints weight = 198344.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028086 restraints weight = 136270.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.028603 restraints weight = 101613.281| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22782 Z= 0.217 Angle : 0.808 26.963 30766 Z= 0.398 Chirality : 0.151 1.773 3518 Planarity : 0.004 0.060 3921 Dihedral : 11.192 152.437 3341 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.27 % Favored : 93.69 % Rotamer: Outliers : 0.62 % Allowed : 10.83 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 2806 helix: -0.77 (0.13), residues: 1305 sheet: -1.92 (0.26), residues: 337 loop : -2.13 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 337 TYR 0.015 0.002 TYR A 502 PHE 0.024 0.002 PHE F 576 TRP 0.021 0.001 TRP B 213 HIS 0.009 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00438 (22781) covalent geometry : angle 0.80847 (30766) hydrogen bonds : bond 0.04340 ( 900) hydrogen bonds : angle 5.55398 ( 2649) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.944 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: 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: A 372 MET cc_start: 0.9452 (ptp) cc_final: 0.9206 (ptp) REVERT: A 393 MET cc_start: 0.9157 (tpp) cc_final: 0.8890 (tpp) REVERT: A 657 MET cc_start: 0.9498 (tpp) cc_final: 0.9251 (tpp) REVERT: A 724 TYR cc_start: 0.8924 (m-80) cc_final: 0.8562 (m-80) REVERT: B 248 MET cc_start: 0.9575 (ttm) cc_final: 0.9186 (tpp) REVERT: B 573 MET cc_start: 0.9041 (ptp) cc_final: 0.8774 (ptp) REVERT: C 414 MET cc_start: 0.8859 (mmp) cc_final: 0.8080 (mmp) REVERT: C 657 MET cc_start: 0.9475 (tpp) cc_final: 0.8779 (mmm) REVERT: C 712 MET cc_start: 0.8675 (tmm) cc_final: 0.7657 (tmm) REVERT: C 716 MET cc_start: 0.9400 (mtp) cc_final: 0.9005 (mtp) REVERT: D 327 PHE cc_start: 0.9056 (t80) cc_final: 0.8396 (t80) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.3549 time to fit residues: 74.2699 Evaluate side-chains 131 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 71 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 ASN D 696 GLN ** E 669 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 = 0.2859 r_free = 0.2859 target = 0.030669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023724 restraints weight = 664216.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.024972 restraints weight = 332678.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.025858 restraints weight = 202419.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026484 restraints weight = 138976.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.026960 restraints weight = 103334.983| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22782 Z= 0.295 Angle : 0.837 25.918 30766 Z= 0.421 Chirality : 0.151 1.772 3518 Planarity : 0.005 0.080 3921 Dihedral : 11.063 159.903 3339 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.20 % Favored : 91.77 % Rotamer: Outliers : 0.99 % Allowed : 11.74 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.15), residues: 2806 helix: -0.88 (0.13), residues: 1319 sheet: -1.90 (0.26), residues: 327 loop : -2.25 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 388 TYR 0.018 0.002 TYR E 499 PHE 0.021 0.002 PHE F 576 TRP 0.016 0.002 TRP B 213 HIS 0.010 0.002 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00571 (22781) covalent geometry : angle 0.83699 (30766) hydrogen bonds : bond 0.04212 ( 900) hydrogen bonds : angle 5.75915 ( 2649) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.332 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: 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: A 248 MET cc_start: 0.9649 (mtp) cc_final: 0.9237 (ptp) REVERT: A 393 MET cc_start: 0.9336 (tpp) cc_final: 0.9103 (tpp) REVERT: A 573 MET cc_start: 0.9322 (ptp) cc_final: 0.9092 (pmm) REVERT: A 585 MET cc_start: 0.9039 (tmm) cc_final: 0.8790 (ppp) REVERT: A 657 MET cc_start: 0.9544 (tpp) cc_final: 0.9338 (tpp) REVERT: A 724 TYR cc_start: 0.9121 (m-80) cc_final: 0.8719 (m-80) REVERT: B 363 GLN cc_start: 0.9585 (tt0) cc_final: 0.9289 (tp40) REVERT: B 573 MET cc_start: 0.9216 (ptp) cc_final: 0.8839 (ptp) REVERT: B 585 MET cc_start: 0.9355 (ttm) cc_final: 0.9044 (tpp) REVERT: C 655 MET cc_start: 0.9488 (mtt) cc_final: 0.9237 (mtt) REVERT: C 657 MET cc_start: 0.9397 (tpp) cc_final: 0.8785 (mmm) REVERT: D 372 MET cc_start: 0.7879 (mpp) cc_final: 0.7625 (mpp) REVERT: E 372 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: F 504 MET cc_start: 0.9125 (pmm) cc_final: 0.8909 (pmm) outliers start: 24 outliers final: 17 residues processed: 140 average time/residue: 0.3665 time to fit residues: 80.2848 Evaluate side-chains 135 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 699 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 62 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 259 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.030264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.023154 restraints weight = 655597.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.024398 restraints weight = 329813.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.025277 restraints weight = 203501.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.025898 restraints weight = 141353.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.026367 restraints weight = 105969.059| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22782 Z= 0.225 Angle : 0.790 27.073 30766 Z= 0.387 Chirality : 0.150 1.790 3518 Planarity : 0.004 0.079 3921 Dihedral : 10.577 158.833 3339 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 0.91 % Allowed : 12.20 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.15), residues: 2806 helix: -0.58 (0.14), residues: 1306 sheet: -1.56 (0.29), residues: 296 loop : -2.17 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.014 0.002 TYR E 499 PHE 0.017 0.002 PHE E 306 TRP 0.015 0.001 TRP B 213 HIS 0.009 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00446 (22781) covalent geometry : angle 0.78995 (30766) hydrogen bonds : bond 0.03852 ( 900) hydrogen bonds : angle 5.50640 ( 2649) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.207 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: 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: A 248 MET cc_start: 0.9630 (mtp) cc_final: 0.9283 (ptp) REVERT: A 393 MET cc_start: 0.9260 (tpp) cc_final: 0.8785 (tpp) REVERT: A 573 MET cc_start: 0.9292 (ptp) cc_final: 0.9055 (pmm) REVERT: A 724 TYR cc_start: 0.9174 (m-80) cc_final: 0.8803 (m-80) REVERT: B 248 MET cc_start: 0.9311 (tpp) cc_final: 0.8908 (tpp) REVERT: B 573 MET cc_start: 0.9177 (ptp) cc_final: 0.8911 (ptp) REVERT: B 585 MET cc_start: 0.9354 (ttm) cc_final: 0.9012 (tpp) REVERT: B 716 MET cc_start: 0.9695 (ttm) cc_final: 0.9461 (mtp) REVERT: C 414 MET cc_start: 0.8758 (mmp) cc_final: 0.7951 (mmp) REVERT: D 372 MET cc_start: 0.8115 (mpp) cc_final: 0.7602 (mpp) REVERT: F 504 MET cc_start: 0.9158 (pmm) cc_final: 0.8897 (pmm) REVERT: F 657 MET cc_start: 0.9669 (tpp) cc_final: 0.9300 (tpp) outliers start: 22 outliers final: 16 residues processed: 137 average time/residue: 0.3830 time to fit residues: 82.4470 Evaluate side-chains 132 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 699 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 100 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.029591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.022658 restraints weight = 643366.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023911 restraints weight = 323251.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.024800 restraints weight = 197519.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.025441 restraints weight = 136029.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.025875 restraints weight = 101203.886| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22782 Z= 0.163 Angle : 0.760 27.255 30766 Z= 0.363 Chirality : 0.150 1.776 3518 Planarity : 0.004 0.059 3921 Dihedral : 10.289 160.283 3339 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 0.83 % Allowed : 12.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.15), residues: 2806 helix: -0.21 (0.14), residues: 1309 sheet: -1.39 (0.30), residues: 296 loop : -2.09 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.011 0.001 TYR B 502 PHE 0.016 0.001 PHE E 306 TRP 0.013 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00341 (22781) covalent geometry : angle 0.76000 (30766) hydrogen bonds : bond 0.03550 ( 900) hydrogen bonds : angle 5.22996 ( 2649) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.259 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: 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: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.9341 (ptp) cc_final: 0.8986 (ptm) REVERT: A 573 MET cc_start: 0.9299 (ptp) cc_final: 0.9060 (pmm) REVERT: A 585 MET cc_start: 0.8912 (tmm) cc_final: 0.8463 (ppp) REVERT: A 724 TYR cc_start: 0.9171 (m-80) cc_final: 0.8794 (m-80) REVERT: B 248 MET cc_start: 0.9272 (tpp) cc_final: 0.8913 (tpp) REVERT: B 573 MET cc_start: 0.9156 (ptp) cc_final: 0.8867 (ptp) REVERT: C 414 MET cc_start: 0.8759 (mmp) cc_final: 0.8072 (mmp) REVERT: C 573 MET cc_start: 0.9237 (ptp) cc_final: 0.9035 (ptp) REVERT: C 655 MET cc_start: 0.9446 (mtt) cc_final: 0.9092 (mtt) REVERT: C 657 MET cc_start: 0.9474 (tpp) cc_final: 0.8782 (mmm) REVERT: D 372 MET cc_start: 0.8346 (mpp) cc_final: 0.7714 (mpp) REVERT: D 712 MET cc_start: 0.9368 (tmm) cc_final: 0.8873 (tmm) REVERT: F 504 MET cc_start: 0.9167 (pmm) cc_final: 0.8876 (pmm) REVERT: F 585 MET cc_start: 0.8900 (ppp) cc_final: 0.8651 (ppp) REVERT: F 630 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9347 (tt) REVERT: F 657 MET cc_start: 0.9680 (tpp) cc_final: 0.9308 (tpp) outliers start: 20 outliers final: 18 residues processed: 139 average time/residue: 0.3756 time to fit residues: 82.3270 Evaluate side-chains 136 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 128 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 142 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.025041 restraints weight = 621030.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.026267 restraints weight = 313910.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.027150 restraints weight = 195227.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027783 restraints weight = 136762.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.028236 restraints weight = 102923.199| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22782 Z= 0.124 Angle : 0.747 27.393 30766 Z= 0.351 Chirality : 0.150 1.785 3518 Planarity : 0.004 0.047 3921 Dihedral : 10.029 163.006 3339 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 0.91 % Allowed : 12.94 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2806 helix: 0.12 (0.14), residues: 1316 sheet: -1.39 (0.29), residues: 303 loop : -1.98 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 385 TYR 0.009 0.001 TYR B 502 PHE 0.014 0.001 PHE E 306 TRP 0.012 0.001 TRP B 213 HIS 0.007 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00280 (22781) covalent geometry : angle 0.74726 (30766) hydrogen bonds : bond 0.03378 ( 900) hydrogen bonds : angle 4.99518 ( 2649) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.337 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: 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: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9584 (mtp) cc_final: 0.9232 (ptp) REVERT: A 573 MET cc_start: 0.9295 (ptp) cc_final: 0.9055 (pmm) REVERT: A 585 MET cc_start: 0.8892 (tmm) cc_final: 0.8451 (ppp) REVERT: B 248 MET cc_start: 0.9217 (tpp) cc_final: 0.8869 (tpp) REVERT: B 573 MET cc_start: 0.9128 (ptp) cc_final: 0.8924 (ptp) REVERT: C 248 MET cc_start: 0.9238 (mtp) cc_final: 0.8705 (ptp) REVERT: C 414 MET cc_start: 0.8722 (mmp) cc_final: 0.8024 (mmp) REVERT: C 573 MET cc_start: 0.9245 (ptp) cc_final: 0.9025 (ptp) REVERT: D 712 MET cc_start: 0.9359 (tmm) cc_final: 0.8872 (tmm) REVERT: E 657 MET cc_start: 0.9139 (mmm) cc_final: 0.8923 (mmm) REVERT: F 504 MET cc_start: 0.9157 (pmm) cc_final: 0.8835 (pmm) REVERT: F 630 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9336 (tt) REVERT: F 657 MET cc_start: 0.9687 (tpp) cc_final: 0.9272 (tpp) outliers start: 22 outliers final: 18 residues processed: 143 average time/residue: 0.3792 time to fit residues: 85.9019 Evaluate side-chains 137 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 217 optimal weight: 30.0000 chunk 223 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 583 GLN B 530 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 719 GLN ** 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 = 0.2822 r_free = 0.2822 target = 0.028867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.022170 restraints weight = 674868.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.023367 restraints weight = 336592.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.024229 restraints weight = 205960.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.024837 restraints weight = 141211.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.025279 restraints weight = 105219.404| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22782 Z= 0.293 Angle : 0.819 26.186 30766 Z= 0.406 Chirality : 0.151 1.809 3518 Planarity : 0.005 0.065 3921 Dihedral : 10.330 170.988 3339 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.56 % Rotamer: Outliers : 1.12 % Allowed : 13.15 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.15), residues: 2806 helix: -0.48 (0.13), residues: 1324 sheet: -1.70 (0.28), residues: 320 loop : -2.21 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 388 TYR 0.021 0.002 TYR D 294 PHE 0.016 0.002 PHE C 618 TRP 0.018 0.002 TRP B 213 HIS 0.010 0.002 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00565 (22781) covalent geometry : angle 0.81885 (30766) hydrogen bonds : bond 0.03800 ( 900) hydrogen bonds : angle 5.52794 ( 2649) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.227 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: 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: A 248 MET cc_start: 0.9625 (mtp) cc_final: 0.9305 (ptp) REVERT: A 573 MET cc_start: 0.9358 (ptp) cc_final: 0.9130 (pmm) REVERT: A 585 MET cc_start: 0.8939 (tmm) cc_final: 0.8564 (ppp) REVERT: A 724 TYR cc_start: 0.9161 (m-80) cc_final: 0.8880 (m-80) REVERT: B 248 MET cc_start: 0.9293 (tpp) cc_final: 0.8933 (tpp) REVERT: B 393 MET cc_start: 0.9078 (mmp) cc_final: 0.8845 (mmp) REVERT: B 453 MET cc_start: 0.9036 (ttm) cc_final: 0.8772 (tmm) REVERT: B 573 MET cc_start: 0.9267 (ptp) cc_final: 0.9059 (ptp) REVERT: C 414 MET cc_start: 0.8716 (mmp) cc_final: 0.7993 (mmp) REVERT: C 657 MET cc_start: 0.9395 (tpp) cc_final: 0.8688 (mmm) REVERT: D 712 MET cc_start: 0.9366 (tmm) cc_final: 0.8930 (tmm) REVERT: F 504 MET cc_start: 0.9143 (pmm) cc_final: 0.8838 (pmm) REVERT: F 657 MET cc_start: 0.9667 (tpp) cc_final: 0.9343 (tpp) outliers start: 27 outliers final: 23 residues processed: 137 average time/residue: 0.3886 time to fit residues: 83.6312 Evaluate side-chains 134 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 699 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.022526 restraints weight = 641455.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.023778 restraints weight = 319169.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.024665 restraints weight = 194005.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.025291 restraints weight = 133265.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.025762 restraints weight = 99039.134| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22782 Z= 0.138 Angle : 0.760 27.109 30766 Z= 0.359 Chirality : 0.150 1.792 3518 Planarity : 0.004 0.061 3921 Dihedral : 9.989 172.386 3339 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.77 % Favored : 92.20 % Rotamer: Outliers : 0.87 % Allowed : 13.48 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.15), residues: 2806 helix: -0.00 (0.14), residues: 1319 sheet: -1.47 (0.29), residues: 304 loop : -2.10 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.010 0.001 TYR D 611 PHE 0.014 0.001 PHE E 306 TRP 0.013 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00303 (22781) covalent geometry : angle 0.76023 (30766) hydrogen bonds : bond 0.03369 ( 900) hydrogen bonds : angle 5.08733 ( 2649) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.304 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: 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: A 248 MET cc_start: 0.9602 (mtp) cc_final: 0.9220 (ptp) REVERT: A 573 MET cc_start: 0.9316 (ptp) cc_final: 0.9080 (pmm) REVERT: A 585 MET cc_start: 0.8938 (tmm) cc_final: 0.8502 (ppp) REVERT: A 655 MET cc_start: 0.9292 (ttp) cc_final: 0.9026 (ptm) REVERT: B 248 MET cc_start: 0.9258 (tpp) cc_final: 0.8899 (tpp) REVERT: C 248 MET cc_start: 0.9294 (mtp) cc_final: 0.8716 (ptp) REVERT: C 414 MET cc_start: 0.8742 (mmp) cc_final: 0.8080 (mmp) REVERT: C 657 MET cc_start: 0.9402 (tpp) cc_final: 0.8685 (mmm) REVERT: D 712 MET cc_start: 0.9367 (tmm) cc_final: 0.8925 (tmm) REVERT: E 453 MET cc_start: 0.9461 (mmm) cc_final: 0.8912 (mmm) REVERT: F 504 MET cc_start: 0.9139 (pmm) cc_final: 0.8827 (pmm) REVERT: F 630 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9342 (tt) REVERT: F 657 MET cc_start: 0.9666 (tpp) cc_final: 0.9345 (tpp) outliers start: 21 outliers final: 18 residues processed: 137 average time/residue: 0.3923 time to fit residues: 84.6153 Evaluate side-chains 135 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 24 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.021927 restraints weight = 658344.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023131 restraints weight = 330690.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.024011 restraints weight = 204140.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.024610 restraints weight = 140876.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.025062 restraints weight = 104792.064| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22782 Z= 0.210 Angle : 0.779 26.699 30766 Z= 0.376 Chirality : 0.150 1.797 3518 Planarity : 0.004 0.053 3921 Dihedral : 9.880 175.486 3339 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.56 % Rotamer: Outliers : 0.91 % Allowed : 13.35 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 2806 helix: -0.14 (0.14), residues: 1330 sheet: -1.59 (0.29), residues: 316 loop : -2.15 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 385 TYR 0.014 0.001 TYR D 611 PHE 0.020 0.002 PHE D 215 TRP 0.015 0.001 TRP B 213 HIS 0.009 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00423 (22781) covalent geometry : angle 0.77942 (30766) hydrogen bonds : bond 0.03456 ( 900) hydrogen bonds : angle 5.24397 ( 2649) Misc. bond : bond 0.00063 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.228 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: 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: A 248 MET cc_start: 0.9593 (mtp) cc_final: 0.9249 (ptp) REVERT: A 573 MET cc_start: 0.9332 (ptp) cc_final: 0.9101 (pmm) REVERT: A 585 MET cc_start: 0.8992 (tmm) cc_final: 0.8577 (ppp) REVERT: A 655 MET cc_start: 0.9282 (ttp) cc_final: 0.9036 (ptm) REVERT: B 248 MET cc_start: 0.9291 (tpp) cc_final: 0.8953 (tpp) REVERT: B 340 MET cc_start: 0.4486 (ttp) cc_final: 0.3565 (tmm) REVERT: B 573 MET cc_start: 0.9092 (ptp) cc_final: 0.8867 (pmm) REVERT: C 414 MET cc_start: 0.8736 (mmp) cc_final: 0.8132 (mmp) REVERT: C 657 MET cc_start: 0.9421 (tpp) cc_final: 0.8735 (mmm) REVERT: D 712 MET cc_start: 0.9382 (tmm) cc_final: 0.8997 (tmm) REVERT: F 630 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9355 (tt) REVERT: F 657 MET cc_start: 0.9696 (tpp) cc_final: 0.9376 (tpp) outliers start: 22 outliers final: 21 residues processed: 132 average time/residue: 0.3992 time to fit residues: 82.8789 Evaluate side-chains 132 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 28 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.029853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.022814 restraints weight = 638023.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024045 restraints weight = 317875.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.024930 restraints weight = 195977.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.025571 restraints weight = 135388.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.026056 restraints weight = 101181.099| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22782 Z= 0.117 Angle : 0.755 27.675 30766 Z= 0.352 Chirality : 0.150 1.777 3518 Planarity : 0.004 0.048 3921 Dihedral : 9.467 171.649 3339 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.74 % Allowed : 13.68 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.16), residues: 2806 helix: 0.36 (0.14), residues: 1328 sheet: -1.24 (0.30), residues: 303 loop : -1.98 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.012 0.001 TYR A 724 PHE 0.012 0.001 PHE E 306 TRP 0.010 0.001 TRP B 213 HIS 0.007 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00274 (22781) covalent geometry : angle 0.75484 (30766) hydrogen bonds : bond 0.03195 ( 900) hydrogen bonds : angle 4.85303 ( 2649) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5303.43 seconds wall clock time: 92 minutes 9.34 seconds (5529.34 seconds total)