Starting phenix.real_space_refine on Thu Dec 26 13:51:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_9103_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_9103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_9103.map" model { file = "/net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_9103_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mdp_9103/12_2024/6mdp_9103_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 22.47, per 1000 atoms: 0.50 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: 12.84 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 3.53 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: 17.51 Time building geometry restraints manager: 14.90 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: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.790 Extract box with map and model: 1.810 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 92.090 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.970 ------------------------------------------------------------------------------- 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 : 0.009 0.091 22781 Z= 0.583 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 : 5.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.003 TRP D 704 HIS 0.043 0.003 HIS A 417 PHE 0.043 0.004 PHE D 231 TYR 0.027 0.003 TYR A 502 ARG 0.019 0.001 ARG A 388 *********************** 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 : 3.820 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: symmetry clash REVERT: A 340 MET cc_start: 0.5494 (pp-130) cc_final: 0.4188 (pp-130) REVERT: C 340 MET cc_start: 0.1768 (mtm) cc_final: 0.0902 (mmt) REVERT: C 573 MET cc_start: 0.4995 (ptp) cc_final: 0.4686 (ptt) outliers start: 8 outliers final: 2 residues processed: 203 average time/residue: 0.9705 time to fit residues: 294.0323 Evaluate side-chains 139 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 3.977 ------------------------------------------------------------------------------- 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 236 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 353 GLN A 363 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 620 ASN D 247 GLN D 278 ASN D 374 ASN D 561 ASN D 675 GLN E 278 ASN E 474 GLN E 486 ASN E 620 ASN E 669 ASN E 675 GLN F 527 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22781 Z= 0.266 Angle : 0.844 27.295 30766 Z= 0.417 Chirality : 0.150 1.786 3518 Planarity : 0.005 0.067 3921 Dihedral : 11.667 164.194 3345 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 0.79 % Allowed : 10.21 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.14), residues: 2806 helix: -1.22 (0.13), residues: 1293 sheet: -2.10 (0.25), residues: 319 loop : -2.19 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 510 HIS 0.009 0.001 HIS D 417 PHE 0.016 0.002 PHE D 231 TYR 0.015 0.002 TYR A 502 ARG 0.008 0.001 ARG A 388 *********************** 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 156 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 3.618 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: 0.5965 (ptp) cc_final: 0.5714 (ptp) REVERT: C 340 MET cc_start: 0.2013 (mtm) cc_final: 0.1241 (mmt) outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 0.8571 time to fit residues: 205.2250 Evaluate side-chains 138 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 420 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22781 Z= 0.278 Angle : 0.805 27.061 30766 Z= 0.395 Chirality : 0.150 1.775 3518 Planarity : 0.004 0.060 3921 Dihedral : 11.338 155.853 3341 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.70 % Allowed : 10.91 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.15), residues: 2806 helix: -0.82 (0.13), residues: 1301 sheet: -1.89 (0.26), residues: 336 loop : -2.16 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 PHE 0.020 0.002 PHE F 576 TYR 0.014 0.002 TYR A 502 ARG 0.005 0.000 ARG B 337 *********************** 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 141 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 4.510 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: A 276 MET cc_start: 0.7699 (ppp) cc_final: 0.7338 (ppp) REVERT: A 585 MET cc_start: 0.6242 (ppp) cc_final: 0.5994 (ppp) REVERT: B 420 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6105 (pp) REVERT: C 340 MET cc_start: 0.1089 (mtm) cc_final: 0.0727 (mmt) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.9129 time to fit residues: 196.1570 Evaluate side-chains 135 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 LEU 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 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 F residue 561 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 242 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22781 Z= 0.202 Angle : 0.766 27.188 30766 Z= 0.366 Chirality : 0.150 1.761 3518 Planarity : 0.004 0.046 3921 Dihedral : 10.720 156.411 3341 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 0.74 % Allowed : 11.58 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 2806 helix: -0.31 (0.14), residues: 1305 sheet: -1.52 (0.28), residues: 315 loop : -2.03 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.007 0.001 HIS D 417 PHE 0.016 0.001 PHE F 576 TYR 0.011 0.001 TYR A 502 ARG 0.004 0.000 ARG B 385 *********************** 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 142 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 3.805 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: A 276 MET cc_start: 0.7611 (ppp) cc_final: 0.7063 (ppp) REVERT: A 585 MET cc_start: 0.6162 (ppp) cc_final: 0.5924 (ppp) REVERT: B 420 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6099 (pp) REVERT: C 340 MET cc_start: 0.1170 (mtm) cc_final: 0.0671 (mmp) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 0.8321 time to fit residues: 184.0016 Evaluate side-chains 133 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 LEU 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 441 LEU Chi-restraints excluded: chain E residue 718 LEU 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 225 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22781 Z= 0.177 Angle : 0.747 27.232 30766 Z= 0.352 Chirality : 0.150 1.767 3518 Planarity : 0.004 0.039 3921 Dihedral : 10.211 165.235 3341 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 0.87 % Allowed : 12.11 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2806 helix: -0.03 (0.14), residues: 1322 sheet: -1.28 (0.29), residues: 304 loop : -1.92 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.006 0.001 HIS D 417 PHE 0.012 0.001 PHE E 306 TYR 0.009 0.001 TYR A 502 ARG 0.003 0.000 ARG B 385 *********************** 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 147 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 276 MET cc_start: 0.7609 (ppp) cc_final: 0.7037 (ppp) REVERT: B 420 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6236 (pp) REVERT: B 712 MET cc_start: 0.6167 (tmm) cc_final: 0.5931 (tmm) REVERT: C 340 MET cc_start: 0.1110 (mtm) cc_final: 0.0542 (mmp) REVERT: F 585 MET cc_start: 0.6744 (ppp) cc_final: 0.6272 (ppp) outliers start: 21 outliers final: 15 residues processed: 146 average time/residue: 0.8383 time to fit residues: 194.0705 Evaluate side-chains 135 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 420 LEU 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 368 LEU 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 441 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** C 669 ASN D 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22781 Z= 0.368 Angle : 0.815 26.368 30766 Z= 0.406 Chirality : 0.151 1.781 3518 Planarity : 0.004 0.068 3921 Dihedral : 10.330 176.917 3341 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.80 % Favored : 92.16 % Rotamer: Outliers : 0.95 % Allowed : 12.28 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2806 helix: -0.50 (0.13), residues: 1324 sheet: -1.56 (0.28), residues: 318 loop : -2.11 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 213 HIS 0.010 0.002 HIS D 417 PHE 0.014 0.002 PHE C 618 TYR 0.013 0.002 TYR F 611 ARG 0.006 0.001 ARG A 388 *********************** 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 139 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 3.879 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 276 MET cc_start: 0.7727 (ppp) cc_final: 0.7097 (ppp) REVERT: A 393 MET cc_start: 0.6765 (tpp) cc_final: 0.6305 (tpp) REVERT: C 340 MET cc_start: 0.2375 (mtm) cc_final: 0.1637 (mmp) REVERT: F 573 MET cc_start: 0.7314 (tpp) cc_final: 0.7110 (tpp) outliers start: 23 outliers final: 21 residues processed: 137 average time/residue: 0.8268 time to fit residues: 177.8257 Evaluate side-chains 135 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 655 MET 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 368 LEU 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 441 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 718 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** B 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** ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22781 Z= 0.292 Angle : 0.778 26.910 30766 Z= 0.378 Chirality : 0.150 1.780 3518 Planarity : 0.004 0.069 3921 Dihedral : 10.275 170.130 3341 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 1.12 % Allowed : 12.28 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2806 helix: -0.40 (0.14), residues: 1321 sheet: -1.59 (0.28), residues: 321 loop : -2.13 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 213 HIS 0.009 0.001 HIS D 417 PHE 0.017 0.002 PHE E 306 TYR 0.011 0.001 TYR D 611 ARG 0.004 0.000 ARG D 271 *********************** 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 143 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 3.605 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 276 MET cc_start: 0.7679 (ppp) cc_final: 0.7047 (ppp) REVERT: C 340 MET cc_start: 0.2462 (mtm) cc_final: 0.1863 (mmp) REVERT: E 393 MET cc_start: 0.6695 (mpp) cc_final: 0.6477 (mpp) outliers start: 27 outliers final: 22 residues processed: 140 average time/residue: 0.8426 time to fit residues: 185.3100 Evaluate side-chains 136 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 627 LEU 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 503 ILE Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 720 MET 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 E residue 718 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 Chi-restraints excluded: chain F residue 699 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22781 Z= 0.224 Angle : 0.766 27.115 30766 Z= 0.364 Chirality : 0.150 1.779 3518 Planarity : 0.004 0.060 3921 Dihedral : 10.030 162.136 3339 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 0.91 % Allowed : 12.82 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2806 helix: -0.07 (0.14), residues: 1316 sheet: -1.41 (0.29), residues: 308 loop : -2.00 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 PHE 0.021 0.001 PHE D 327 TYR 0.010 0.001 TYR A 502 ARG 0.013 0.000 ARG B 280 *********************** 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 137 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 3.660 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: A 276 MET cc_start: 0.7704 (ppp) cc_final: 0.7058 (ppp) REVERT: C 340 MET cc_start: 0.2459 (mtm) cc_final: 0.1796 (mmp) REVERT: E 393 MET cc_start: 0.6636 (mpp) cc_final: 0.6423 (mpp) outliers start: 22 outliers final: 20 residues processed: 135 average time/residue: 0.8007 time to fit residues: 171.1709 Evaluate side-chains 132 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 627 LEU 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 655 MET Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 LEU 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 E residue 718 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 245 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 237 optimal weight: 0.4980 chunk 250 optimal weight: 0.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** E 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22781 Z= 0.218 Angle : 0.761 26.961 30766 Z= 0.361 Chirality : 0.150 1.781 3518 Planarity : 0.004 0.050 3921 Dihedral : 9.858 151.999 3339 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.56 % Favored : 92.41 % Rotamer: Outliers : 0.99 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2806 helix: 0.05 (0.14), residues: 1333 sheet: -1.39 (0.29), residues: 310 loop : -2.02 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 PHE 0.025 0.001 PHE D 327 TYR 0.010 0.001 TYR D 611 ARG 0.007 0.000 ARG B 280 *********************** 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: 24 poor density : 114 time to evaluate : 4.077 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 276 MET cc_start: 0.7631 (ppp) cc_final: 0.7076 (ppp) REVERT: C 340 MET cc_start: 0.2485 (mtm) cc_final: 0.1836 (mmp) outliers start: 24 outliers final: 22 residues processed: 136 average time/residue: 0.8117 time to fit residues: 175.1336 Evaluate side-chains 136 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 627 LEU 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 C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 669 ASN 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 E residue 676 LEU Chi-restraints excluded: chain E residue 718 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 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** C 669 ASN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** E 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22781 Z= 0.399 Angle : 0.845 26.270 30766 Z= 0.421 Chirality : 0.151 1.790 3518 Planarity : 0.005 0.060 3921 Dihedral : 9.952 140.317 3339 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.62 % Favored : 90.34 % Rotamer: Outliers : 0.91 % Allowed : 13.06 % Favored : 86.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.15), residues: 2806 helix: -0.60 (0.13), residues: 1328 sheet: -1.71 (0.28), residues: 323 loop : -2.25 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 213 HIS 0.010 0.002 HIS D 417 PHE 0.023 0.002 PHE D 327 TYR 0.017 0.002 TYR D 611 ARG 0.006 0.001 ARG B 280 ********************** 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 133 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 3.842 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: A 276 MET cc_start: 0.7669 (ppp) cc_final: 0.7095 (ppp) outliers start: 22 outliers final: 21 residues processed: 132 average time/residue: 0.8304 time to fit residues: 174.0368 Evaluate side-chains 131 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL 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 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 368 LEU Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain D residue 253 VAL 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 E residue 718 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 Chi-restraints excluded: chain F residue 699 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** 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 = 0.2852 r_free = 0.2852 target = 0.029776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.022824 restraints weight = 642405.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.024065 restraints weight = 320531.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.024962 restraints weight = 196710.047| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22781 Z= 0.204 Angle : 0.771 27.032 30766 Z= 0.364 Chirality : 0.151 1.793 3518 Planarity : 0.004 0.063 3921 Dihedral : 9.713 138.861 3339 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.30 % Rotamer: Outliers : 0.79 % Allowed : 13.31 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 2806 helix: -0.07 (0.14), residues: 1341 sheet: -1.33 (0.30), residues: 298 loop : -2.09 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 213 HIS 0.008 0.001 HIS D 417 PHE 0.026 0.002 PHE D 327 TYR 0.011 0.001 TYR D 611 ARG 0.007 0.000 ARG D 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6500.34 seconds wall clock time: 119 minutes 27.04 seconds (7167.04 seconds total)