Starting phenix.real_space_refine on Sun Sep 29 00:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/09_2024/6dvw_8919.cif" } resolution = 4.3 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 13648 2.51 5 N 3480 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21004 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Restraints were copied for chains: C, B, D Time building chain proxies: 11.68, per 1000 atoms: 0.56 Number of scatterers: 21004 At special positions: 0 Unit cell: (141.48, 141.48, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3752 8.00 N 3480 7.00 C 13648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.6 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 62.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 117 through 130 removed outlier: 4.437A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.008A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.900A pdb=" N PHE A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 251 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.701A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.611A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.798A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.516A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 501 removed outlier: 4.077A pdb=" N LEU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.504A pdb=" N GLN A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.745A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.724A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.437A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.695A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.210A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.899A pdb=" N PHE B 250 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 251 " --> pdb=" O VAL B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 251' Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.610A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.650A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.607A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.516A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.505A pdb=" N GLN B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.744A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.725A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 612' Processing helix chain 'B' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 removed outlier: 4.438A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 5.129A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 removed outlier: 3.800A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.900A pdb=" N PHE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 251' Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.609A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.517A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.504A pdb=" N GLN C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.744A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.725A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 4.438A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU D 214 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.899A pdb=" N PHE D 250 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D 251 " --> pdb=" O VAL D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 251' Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.610A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.517A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 457 removed outlier: 3.994A pdb=" N LEU D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.329A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 515 removed outlier: 3.505A pdb=" N GLN D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.745A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.724A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.052A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 612 removed outlier: 4.081A pdb=" N LYS D 611 " --> pdb=" O SER D 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 607 through 612' Processing helix chain 'D' and resid 623 through 638 removed outlier: 4.173A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 656 Processing helix chain 'D' and resid 658 through 676 removed outlier: 3.550A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET D 672 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 790 hydrogen bonds defined for protein. 2292 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: 5.50 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5462 1.33 - 1.45: 4186 1.45 - 1.57: 11604 1.57 - 1.69: 4 1.69 - 1.81: 204 Bond restraints: 21460 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.390 -0.057 2.34e-02 1.83e+03 5.83e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.82e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.78e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.75e+00 bond pdb=" CG ARG D 733 " pdb=" CD ARG D 733 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.89e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 27229 2.22 - 4.45: 1438 4.45 - 6.67: 297 6.67 - 8.89: 44 8.89 - 11.11: 24 Bond angle restraints: 29032 Sorted by residual: angle pdb=" C SER D 613 " pdb=" N LYS D 614 " pdb=" CA LYS D 614 " ideal model delta sigma weight residual 121.54 132.65 -11.11 1.91e+00 2.74e-01 3.39e+01 angle pdb=" C SER A 613 " pdb=" N LYS A 614 " pdb=" CA LYS A 614 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 angle pdb=" C SER C 613 " pdb=" N LYS C 614 " pdb=" CA LYS C 614 " ideal model delta sigma weight residual 121.54 132.60 -11.06 1.91e+00 2.74e-01 3.35e+01 angle pdb=" C SER B 613 " pdb=" N LYS B 614 " pdb=" CA LYS B 614 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" C GLY A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 ... (remaining 29027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 11680 14.96 - 29.91: 925 29.91 - 44.87: 203 44.87 - 59.82: 32 59.82 - 74.78: 16 Dihedral angle restraints: 12856 sinusoidal: 5252 harmonic: 7604 Sorted by residual: dihedral pdb=" CA LYS C 614 " pdb=" C LYS C 614 " pdb=" N ASP C 615 " pdb=" CA ASP C 615 " ideal model delta harmonic sigma weight residual 180.00 -128.09 -51.91 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA LYS D 614 " pdb=" C LYS D 614 " pdb=" N ASP D 615 " pdb=" CA ASP D 615 " ideal model delta harmonic sigma weight residual -180.00 -128.10 -51.90 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA LYS B 614 " pdb=" C LYS B 614 " pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta harmonic sigma weight residual 180.00 -128.10 -51.90 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2485 0.063 - 0.126: 700 0.126 - 0.188: 79 0.188 - 0.251: 36 0.251 - 0.314: 8 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB ILE B 756 " pdb=" CA ILE B 756 " pdb=" CG1 ILE B 756 " pdb=" CG2 ILE B 756 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE C 756 " pdb=" CA ILE C 756 " pdb=" CG1 ILE C 756 " pdb=" CG2 ILE C 756 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE A 756 " pdb=" CA ILE A 756 " pdb=" CG1 ILE A 756 " pdb=" CG2 ILE A 756 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3305 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 368 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO A 369 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 368 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO C 369 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 368 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 369 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 369 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 369 " 0.046 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 90 2.45 - 3.06: 12785 3.06 - 3.68: 30723 3.68 - 4.29: 43034 4.29 - 4.90: 66661 Nonbonded interactions: 153293 Sorted by model distance: nonbonded pdb=" SG CYS C 612 " pdb=" OG1 THR C 649 " model vdw 1.840 3.400 nonbonded pdb=" SG CYS D 612 " pdb=" OG1 THR D 649 " model vdw 1.841 3.400 nonbonded pdb=" SG CYS B 612 " pdb=" OG1 THR B 649 " model vdw 1.841 3.400 nonbonded pdb=" SG CYS A 612 " pdb=" OG1 THR A 649 " model vdw 1.841 3.400 nonbonded pdb=" O LEU A 608 " pdb=" OG SER A 613 " model vdw 2.212 3.040 ... (remaining 153288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.440 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 43.060 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.008 0.066 21460 Z= 0.537 Angle : 1.191 11.113 29032 Z= 0.645 Chirality : 0.061 0.314 3308 Planarity : 0.008 0.081 3624 Dihedral : 11.878 74.777 7920 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.89 % Favored : 83.72 % Rotamer: Outliers : 0.87 % Allowed : 5.74 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -5.79 (0.12), residues: 2568 helix: -3.94 (0.08), residues: 1256 sheet: -4.64 (0.29), residues: 68 loop : -3.68 (0.15), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 380 HIS 0.009 0.002 HIS C 160 PHE 0.024 0.003 PHE D 656 TYR 0.019 0.003 TYR D 439 ARG 0.014 0.002 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 765 time to evaluate : 2.191 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: A 141 ASP cc_start: 0.8572 (m-30) cc_final: 0.8161 (p0) REVERT: A 173 MET cc_start: 0.8589 (mtm) cc_final: 0.8037 (mtt) REVERT: A 198 ASP cc_start: 0.7977 (m-30) cc_final: 0.7149 (t70) REVERT: A 216 GLN cc_start: 0.8519 (tp-100) cc_final: 0.7534 (tp40) REVERT: A 220 ASN cc_start: 0.9122 (m-40) cc_final: 0.8809 (m-40) REVERT: A 221 ILE cc_start: 0.9698 (tp) cc_final: 0.9425 (tp) REVERT: A 251 ASN cc_start: 0.8291 (t0) cc_final: 0.7792 (t0) REVERT: A 268 LEU cc_start: 0.9418 (tp) cc_final: 0.9069 (tp) REVERT: A 335 THR cc_start: 0.9115 (p) cc_final: 0.8407 (t) REVERT: A 346 GLN cc_start: 0.9022 (mt0) cc_final: 0.8578 (mt0) REVERT: A 439 TYR cc_start: 0.8320 (m-80) cc_final: 0.8081 (m-80) REVERT: A 446 CYS cc_start: 0.8737 (m) cc_final: 0.8163 (t) REVERT: A 453 ILE cc_start: 0.9527 (mt) cc_final: 0.9325 (mm) REVERT: A 603 VAL cc_start: 0.9266 (t) cc_final: 0.8899 (p) REVERT: A 627 ASP cc_start: 0.8692 (t0) cc_final: 0.8443 (p0) REVERT: A 639 LEU cc_start: 0.8262 (tp) cc_final: 0.7724 (tp) REVERT: A 672 MET cc_start: 0.7937 (ttp) cc_final: 0.7728 (tmm) REVERT: A 696 ARG cc_start: 0.8950 (ttm170) cc_final: 0.8524 (ttm170) REVERT: A 705 LYS cc_start: 0.9089 (mttt) cc_final: 0.8829 (mttp) REVERT: A 706 MET cc_start: 0.8006 (tmm) cc_final: 0.7175 (tmm) REVERT: A 707 LEU cc_start: 0.6159 (mt) cc_final: 0.5215 (mt) REVERT: B 141 ASP cc_start: 0.8550 (m-30) cc_final: 0.8158 (p0) REVERT: B 173 MET cc_start: 0.8572 (mtm) cc_final: 0.8022 (mtt) REVERT: B 198 ASP cc_start: 0.7979 (m-30) cc_final: 0.7147 (t70) REVERT: B 216 GLN cc_start: 0.8515 (tp-100) cc_final: 0.7534 (tp40) REVERT: B 220 ASN cc_start: 0.9124 (m-40) cc_final: 0.8806 (m-40) REVERT: B 221 ILE cc_start: 0.9700 (tp) cc_final: 0.9425 (tp) REVERT: B 251 ASN cc_start: 0.8305 (t0) cc_final: 0.7833 (t0) REVERT: B 268 LEU cc_start: 0.9429 (tp) cc_final: 0.9047 (tp) REVERT: B 335 THR cc_start: 0.9106 (p) cc_final: 0.8438 (t) REVERT: B 346 GLN cc_start: 0.9037 (mt0) cc_final: 0.8618 (mt0) REVERT: B 439 TYR cc_start: 0.8390 (m-80) cc_final: 0.8164 (m-80) REVERT: B 446 CYS cc_start: 0.8814 (m) cc_final: 0.8201 (t) REVERT: B 603 VAL cc_start: 0.9273 (t) cc_final: 0.8831 (p) REVERT: B 639 LEU cc_start: 0.8236 (tp) cc_final: 0.7712 (tp) REVERT: B 696 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8538 (ttm170) REVERT: B 705 LYS cc_start: 0.9089 (mttt) cc_final: 0.8828 (mttp) REVERT: B 706 MET cc_start: 0.7994 (tmm) cc_final: 0.7136 (tmm) REVERT: B 707 LEU cc_start: 0.6142 (mt) cc_final: 0.5185 (mt) REVERT: B 717 MET cc_start: 0.8087 (tpt) cc_final: 0.7882 (tpp) REVERT: C 141 ASP cc_start: 0.8514 (m-30) cc_final: 0.8084 (p0) REVERT: C 173 MET cc_start: 0.8547 (mtm) cc_final: 0.7991 (mtt) REVERT: C 198 ASP cc_start: 0.7976 (m-30) cc_final: 0.7135 (t70) REVERT: C 216 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7530 (tp40) REVERT: C 220 ASN cc_start: 0.9147 (m-40) cc_final: 0.8834 (m-40) REVERT: C 221 ILE cc_start: 0.9701 (tp) cc_final: 0.9438 (tp) REVERT: C 223 ILE cc_start: 0.9714 (mt) cc_final: 0.9506 (mm) REVERT: C 251 ASN cc_start: 0.8243 (t0) cc_final: 0.7754 (t0) REVERT: C 268 LEU cc_start: 0.9406 (tp) cc_final: 0.9013 (tp) REVERT: C 335 THR cc_start: 0.9136 (p) cc_final: 0.8491 (t) REVERT: C 346 GLN cc_start: 0.9042 (mt0) cc_final: 0.8613 (mt0) REVERT: C 392 LEU cc_start: 0.8455 (tp) cc_final: 0.8219 (tp) REVERT: C 446 CYS cc_start: 0.8761 (m) cc_final: 0.8180 (t) REVERT: C 603 VAL cc_start: 0.9285 (t) cc_final: 0.8968 (p) REVERT: C 627 ASP cc_start: 0.8684 (t0) cc_final: 0.8426 (p0) REVERT: C 639 LEU cc_start: 0.8311 (tp) cc_final: 0.7775 (tp) REVERT: C 705 LYS cc_start: 0.9090 (mttt) cc_final: 0.8827 (mttp) REVERT: C 706 MET cc_start: 0.7989 (tmm) cc_final: 0.7139 (tmm) REVERT: C 707 LEU cc_start: 0.6140 (mt) cc_final: 0.5191 (mt) REVERT: C 717 MET cc_start: 0.8103 (tpt) cc_final: 0.7878 (tpp) REVERT: D 141 ASP cc_start: 0.8589 (m-30) cc_final: 0.8185 (p0) REVERT: D 173 MET cc_start: 0.8595 (mtm) cc_final: 0.8119 (mtt) REVERT: D 198 ASP cc_start: 0.7985 (m-30) cc_final: 0.7139 (t70) REVERT: D 200 LEU cc_start: 0.9410 (tp) cc_final: 0.9141 (mt) REVERT: D 216 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7559 (tp40) REVERT: D 220 ASN cc_start: 0.9163 (m-40) cc_final: 0.8785 (m-40) REVERT: D 221 ILE cc_start: 0.9702 (tp) cc_final: 0.9433 (tp) REVERT: D 251 ASN cc_start: 0.8245 (t0) cc_final: 0.7743 (t0) REVERT: D 268 LEU cc_start: 0.9388 (tp) cc_final: 0.9046 (tp) REVERT: D 293 ASP cc_start: 0.8340 (t0) cc_final: 0.8135 (t0) REVERT: D 335 THR cc_start: 0.9151 (p) cc_final: 0.8472 (t) REVERT: D 346 GLN cc_start: 0.9022 (mt0) cc_final: 0.8602 (mt0) REVERT: D 392 LEU cc_start: 0.8460 (tp) cc_final: 0.8242 (tp) REVERT: D 446 CYS cc_start: 0.8755 (m) cc_final: 0.8170 (t) REVERT: D 639 LEU cc_start: 0.8334 (tp) cc_final: 0.7803 (tp) REVERT: D 672 MET cc_start: 0.8002 (ttp) cc_final: 0.7676 (ttp) REVERT: D 705 LYS cc_start: 0.9089 (mttt) cc_final: 0.8826 (mttp) REVERT: D 706 MET cc_start: 0.8000 (tmm) cc_final: 0.7151 (tmm) REVERT: D 707 LEU cc_start: 0.6190 (mt) cc_final: 0.5247 (mt) REVERT: D 717 MET cc_start: 0.8117 (tpt) cc_final: 0.7858 (tpp) outliers start: 20 outliers final: 8 residues processed: 773 average time/residue: 0.2944 time to fit residues: 355.0128 Evaluate side-chains 508 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 500 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 643 ASN A 671 ASN B 251 ASN B 643 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 643 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 643 ASN D 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21460 Z= 0.217 Angle : 0.801 8.983 29032 Z= 0.416 Chirality : 0.045 0.247 3308 Planarity : 0.006 0.071 3624 Dihedral : 7.204 49.811 2808 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.20 % Favored : 86.64 % Rotamer: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -4.42 (0.14), residues: 2568 helix: -2.40 (0.11), residues: 1404 sheet: -4.58 (0.33), residues: 76 loop : -3.48 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 739 HIS 0.003 0.001 HIS D 426 PHE 0.015 0.001 PHE D 527 TYR 0.012 0.001 TYR D 208 ARG 0.005 0.001 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 719 time to evaluate : 2.347 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: A 173 MET cc_start: 0.8784 (mtm) cc_final: 0.8276 (mtt) REVERT: A 198 ASP cc_start: 0.8186 (m-30) cc_final: 0.7219 (t70) REVERT: A 216 GLN cc_start: 0.8595 (tp-100) cc_final: 0.7991 (tp40) REVERT: A 251 ASN cc_start: 0.7983 (t0) cc_final: 0.7767 (t0) REVERT: A 257 GLU cc_start: 0.7679 (pt0) cc_final: 0.7420 (pt0) REVERT: A 332 GLU cc_start: 0.6925 (pt0) cc_final: 0.6683 (pp20) REVERT: A 335 THR cc_start: 0.8998 (p) cc_final: 0.8368 (t) REVERT: A 346 GLN cc_start: 0.8870 (mt0) cc_final: 0.8611 (mt0) REVERT: A 446 CYS cc_start: 0.8717 (m) cc_final: 0.8486 (t) REVERT: A 695 GLN cc_start: 0.8438 (mt0) cc_final: 0.8090 (mt0) REVERT: A 740 THR cc_start: 0.6687 (m) cc_final: 0.6464 (m) REVERT: B 173 MET cc_start: 0.8773 (mtm) cc_final: 0.8262 (mtt) REVERT: B 198 ASP cc_start: 0.8194 (m-30) cc_final: 0.7217 (t70) REVERT: B 216 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8011 (tp40) REVERT: B 251 ASN cc_start: 0.7992 (t0) cc_final: 0.7781 (t0) REVERT: B 257 GLU cc_start: 0.7695 (pt0) cc_final: 0.7412 (pt0) REVERT: B 332 GLU cc_start: 0.6951 (pt0) cc_final: 0.6649 (pp20) REVERT: B 335 THR cc_start: 0.9000 (p) cc_final: 0.8384 (t) REVERT: B 346 GLN cc_start: 0.8866 (mt0) cc_final: 0.8623 (mt0) REVERT: B 446 CYS cc_start: 0.8730 (m) cc_final: 0.8506 (t) REVERT: B 695 GLN cc_start: 0.8445 (mt0) cc_final: 0.8091 (mt0) REVERT: B 722 LYS cc_start: 0.7219 (tptp) cc_final: 0.6995 (tptp) REVERT: B 740 THR cc_start: 0.6690 (m) cc_final: 0.6437 (m) REVERT: C 173 MET cc_start: 0.8730 (mtm) cc_final: 0.8187 (mtt) REVERT: C 198 ASP cc_start: 0.8212 (m-30) cc_final: 0.7215 (t70) REVERT: C 216 GLN cc_start: 0.8569 (tp-100) cc_final: 0.7974 (tp40) REVERT: C 251 ASN cc_start: 0.8001 (t0) cc_final: 0.7761 (t0) REVERT: C 257 GLU cc_start: 0.7688 (pt0) cc_final: 0.7431 (pt0) REVERT: C 332 GLU cc_start: 0.6973 (pt0) cc_final: 0.6689 (pp20) REVERT: C 335 THR cc_start: 0.9006 (p) cc_final: 0.8382 (t) REVERT: C 346 GLN cc_start: 0.8916 (mt0) cc_final: 0.8674 (mt0) REVERT: C 695 GLN cc_start: 0.8415 (mt0) cc_final: 0.8080 (mt0) REVERT: C 710 TRP cc_start: 0.7669 (m100) cc_final: 0.7419 (m100) REVERT: C 740 THR cc_start: 0.6708 (m) cc_final: 0.6470 (m) REVERT: D 173 MET cc_start: 0.8752 (mtm) cc_final: 0.8203 (mtt) REVERT: D 198 ASP cc_start: 0.8204 (m-30) cc_final: 0.7228 (t70) REVERT: D 216 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8006 (tp40) REVERT: D 251 ASN cc_start: 0.7959 (t0) cc_final: 0.7731 (t0) REVERT: D 285 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8647 (pp20) REVERT: D 332 GLU cc_start: 0.7000 (pt0) cc_final: 0.6722 (pp20) REVERT: D 335 THR cc_start: 0.9013 (p) cc_final: 0.8384 (t) REVERT: D 346 GLN cc_start: 0.8917 (mt0) cc_final: 0.8663 (mt0) REVERT: D 672 MET cc_start: 0.7756 (ttp) cc_final: 0.7197 (ttm) REVERT: D 695 GLN cc_start: 0.8391 (mt0) cc_final: 0.8083 (mt0) REVERT: D 710 TRP cc_start: 0.7676 (m100) cc_final: 0.7435 (m100) REVERT: D 717 MET cc_start: 0.7722 (tpt) cc_final: 0.6856 (tmm) REVERT: D 720 LEU cc_start: 0.8447 (mp) cc_final: 0.8222 (mp) REVERT: D 740 THR cc_start: 0.6715 (m) cc_final: 0.6484 (m) outliers start: 4 outliers final: 0 residues processed: 723 average time/residue: 0.2907 time to fit residues: 329.6696 Evaluate side-chains 506 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 186 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21460 Z= 0.239 Angle : 0.738 8.786 29032 Z= 0.388 Chirality : 0.044 0.261 3308 Planarity : 0.005 0.065 3624 Dihedral : 6.783 48.612 2808 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.25 % Favored : 85.59 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.78 (0.15), residues: 2568 helix: -1.68 (0.12), residues: 1412 sheet: -4.52 (0.35), residues: 72 loop : -3.49 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 692 HIS 0.003 0.001 HIS A 477 PHE 0.017 0.001 PHE A 261 TYR 0.016 0.002 TYR B 382 ARG 0.005 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8942 (p) cc_final: 0.8690 (p) REVERT: A 173 MET cc_start: 0.8749 (mtm) cc_final: 0.8289 (mtt) REVERT: A 198 ASP cc_start: 0.8091 (m-30) cc_final: 0.7183 (t70) REVERT: A 261 PHE cc_start: 0.6971 (m-10) cc_final: 0.6580 (m-80) REVERT: A 268 LEU cc_start: 0.9628 (tp) cc_final: 0.9282 (tp) REVERT: A 335 THR cc_start: 0.8987 (p) cc_final: 0.8364 (t) REVERT: A 346 GLN cc_start: 0.8897 (mt0) cc_final: 0.8626 (mt0) REVERT: A 371 ARG cc_start: 0.8471 (ptt90) cc_final: 0.8126 (ttp80) REVERT: A 488 MET cc_start: 0.8132 (ptp) cc_final: 0.7829 (ptp) REVERT: A 574 MET cc_start: 0.8670 (mmt) cc_final: 0.8076 (mmm) REVERT: A 639 LEU cc_start: 0.8215 (tp) cc_final: 0.7738 (tp) REVERT: A 672 MET cc_start: 0.7232 (tmm) cc_final: 0.6796 (tmm) REVERT: A 710 TRP cc_start: 0.7537 (m100) cc_final: 0.7252 (m100) REVERT: A 740 THR cc_start: 0.6511 (m) cc_final: 0.6247 (m) REVERT: B 171 CYS cc_start: 0.8930 (p) cc_final: 0.8688 (p) REVERT: B 173 MET cc_start: 0.8756 (mtm) cc_final: 0.8273 (mtt) REVERT: B 198 ASP cc_start: 0.8102 (m-30) cc_final: 0.7175 (t70) REVERT: B 261 PHE cc_start: 0.7030 (m-10) cc_final: 0.6599 (m-80) REVERT: B 268 LEU cc_start: 0.9616 (tp) cc_final: 0.9244 (tp) REVERT: B 335 THR cc_start: 0.9013 (p) cc_final: 0.8353 (t) REVERT: B 346 GLN cc_start: 0.8911 (mt0) cc_final: 0.8650 (mt0) REVERT: B 446 CYS cc_start: 0.8746 (m) cc_final: 0.8526 (t) REVERT: B 488 MET cc_start: 0.8152 (ptp) cc_final: 0.7879 (ptp) REVERT: B 574 MET cc_start: 0.8689 (mmt) cc_final: 0.8069 (mmm) REVERT: B 639 LEU cc_start: 0.8075 (tp) cc_final: 0.7724 (tp) REVERT: B 710 TRP cc_start: 0.7703 (m100) cc_final: 0.7474 (m100) REVERT: B 722 LYS cc_start: 0.7337 (tptp) cc_final: 0.7002 (tptp) REVERT: B 740 THR cc_start: 0.6558 (m) cc_final: 0.5826 (m) REVERT: C 171 CYS cc_start: 0.8974 (p) cc_final: 0.8712 (p) REVERT: C 173 MET cc_start: 0.8671 (mtm) cc_final: 0.8177 (mtt) REVERT: C 198 ASP cc_start: 0.8128 (m-30) cc_final: 0.7180 (t70) REVERT: C 221 ILE cc_start: 0.9693 (tp) cc_final: 0.9466 (mm) REVERT: C 293 ASP cc_start: 0.8041 (t0) cc_final: 0.7705 (t0) REVERT: C 332 GLU cc_start: 0.6943 (pt0) cc_final: 0.6670 (pp20) REVERT: C 335 THR cc_start: 0.8987 (p) cc_final: 0.8334 (t) REVERT: C 346 GLN cc_start: 0.8916 (mt0) cc_final: 0.8664 (mt0) REVERT: C 371 ARG cc_start: 0.8468 (ptt90) cc_final: 0.8132 (ttp80) REVERT: C 488 MET cc_start: 0.8106 (ptp) cc_final: 0.7698 (ptp) REVERT: C 574 MET cc_start: 0.8700 (mmt) cc_final: 0.8099 (mmm) REVERT: C 639 LEU cc_start: 0.8047 (tp) cc_final: 0.7680 (tp) REVERT: C 676 LEU cc_start: 0.9246 (mp) cc_final: 0.8899 (mp) REVERT: C 740 THR cc_start: 0.6599 (m) cc_final: 0.5837 (m) REVERT: D 171 CYS cc_start: 0.8980 (p) cc_final: 0.8736 (p) REVERT: D 173 MET cc_start: 0.8682 (mtm) cc_final: 0.8212 (mtt) REVERT: D 198 ASP cc_start: 0.8215 (m-30) cc_final: 0.7224 (t70) REVERT: D 221 ILE cc_start: 0.9693 (tp) cc_final: 0.9487 (mm) REVERT: D 261 PHE cc_start: 0.7084 (m-10) cc_final: 0.6539 (m-80) REVERT: D 268 LEU cc_start: 0.9583 (tp) cc_final: 0.9308 (tp) REVERT: D 293 ASP cc_start: 0.8044 (t0) cc_final: 0.7658 (t0) REVERT: D 332 GLU cc_start: 0.6901 (pt0) cc_final: 0.6696 (pp20) REVERT: D 335 THR cc_start: 0.8993 (p) cc_final: 0.8385 (t) REVERT: D 346 GLN cc_start: 0.8918 (mt0) cc_final: 0.8611 (mt0) REVERT: D 574 MET cc_start: 0.8629 (mmt) cc_final: 0.8047 (mmm) REVERT: D 631 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 639 LEU cc_start: 0.8089 (tp) cc_final: 0.7853 (tp) REVERT: D 672 MET cc_start: 0.7982 (ttp) cc_final: 0.7396 (ttm) REVERT: D 717 MET cc_start: 0.7840 (tpt) cc_final: 0.7581 (tpp) REVERT: D 740 THR cc_start: 0.6554 (m) cc_final: 0.5835 (m) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.2873 time to fit residues: 288.3810 Evaluate side-chains 486 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 671 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21460 Z= 0.277 Angle : 0.749 10.007 29032 Z= 0.391 Chirality : 0.045 0.235 3308 Planarity : 0.005 0.061 3624 Dihedral : 6.638 48.435 2808 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.98 % Favored : 85.86 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.34 (0.15), residues: 2568 helix: -1.17 (0.13), residues: 1388 sheet: -4.32 (0.37), residues: 72 loop : -3.50 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 493 HIS 0.003 0.001 HIS D 160 PHE 0.030 0.001 PHE A 259 TYR 0.018 0.002 TYR A 208 ARG 0.004 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 607 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8157 (mmt) cc_final: 0.7635 (mtt) REVERT: A 171 CYS cc_start: 0.8890 (p) cc_final: 0.8583 (p) REVERT: A 173 MET cc_start: 0.8674 (mtm) cc_final: 0.8261 (mtt) REVERT: A 198 ASP cc_start: 0.8119 (m-30) cc_final: 0.7162 (t70) REVERT: A 268 LEU cc_start: 0.9604 (tp) cc_final: 0.9339 (tp) REVERT: A 322 ASP cc_start: 0.8623 (t70) cc_final: 0.8333 (t0) REVERT: A 335 THR cc_start: 0.9008 (p) cc_final: 0.8357 (t) REVERT: A 346 GLN cc_start: 0.8940 (mt0) cc_final: 0.8646 (mt0) REVERT: A 371 ARG cc_start: 0.8485 (ptt90) cc_final: 0.8191 (ttp80) REVERT: A 488 MET cc_start: 0.8125 (ptp) cc_final: 0.7807 (ptp) REVERT: A 631 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 639 LEU cc_start: 0.8194 (tp) cc_final: 0.7331 (tp) REVERT: B 159 MET cc_start: 0.8156 (mmt) cc_final: 0.7651 (mtt) REVERT: B 171 CYS cc_start: 0.8873 (p) cc_final: 0.8591 (p) REVERT: B 173 MET cc_start: 0.8685 (mtm) cc_final: 0.8231 (mtt) REVERT: B 198 ASP cc_start: 0.8130 (m-30) cc_final: 0.7169 (t70) REVERT: B 268 LEU cc_start: 0.9585 (tp) cc_final: 0.9355 (tp) REVERT: B 322 ASP cc_start: 0.8512 (t70) cc_final: 0.7899 (t0) REVERT: B 335 THR cc_start: 0.8971 (p) cc_final: 0.8305 (t) REVERT: B 346 GLN cc_start: 0.8920 (mt0) cc_final: 0.8668 (mt0) REVERT: B 488 MET cc_start: 0.8179 (ptp) cc_final: 0.7864 (ptp) REVERT: B 631 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 639 LEU cc_start: 0.8143 (tp) cc_final: 0.7493 (tp) REVERT: B 706 MET cc_start: 0.8553 (tpp) cc_final: 0.8101 (tpp) REVERT: B 722 LYS cc_start: 0.6410 (tptm) cc_final: 0.5922 (tptm) REVERT: C 159 MET cc_start: 0.8182 (mmt) cc_final: 0.7719 (mtt) REVERT: C 171 CYS cc_start: 0.8891 (p) cc_final: 0.8593 (p) REVERT: C 173 MET cc_start: 0.8632 (mtm) cc_final: 0.8206 (mtt) REVERT: C 198 ASP cc_start: 0.8165 (m-30) cc_final: 0.7169 (t70) REVERT: C 268 LEU cc_start: 0.9475 (tp) cc_final: 0.9269 (tp) REVERT: C 332 GLU cc_start: 0.6922 (pt0) cc_final: 0.6694 (pp20) REVERT: C 335 THR cc_start: 0.8982 (p) cc_final: 0.8378 (t) REVERT: C 346 GLN cc_start: 0.8933 (mt0) cc_final: 0.8670 (mt0) REVERT: C 371 ARG cc_start: 0.8474 (ptt90) cc_final: 0.8192 (ttp80) REVERT: C 488 MET cc_start: 0.8158 (ptp) cc_final: 0.7787 (ptp) REVERT: C 706 MET cc_start: 0.8589 (tpp) cc_final: 0.8078 (tpp) REVERT: D 159 MET cc_start: 0.8192 (mmt) cc_final: 0.7753 (mtt) REVERT: D 171 CYS cc_start: 0.8884 (p) cc_final: 0.8570 (p) REVERT: D 173 MET cc_start: 0.8636 (mtm) cc_final: 0.8162 (mtt) REVERT: D 198 ASP cc_start: 0.8238 (m-30) cc_final: 0.7211 (t70) REVERT: D 268 LEU cc_start: 0.9583 (tp) cc_final: 0.9231 (tp) REVERT: D 322 ASP cc_start: 0.8598 (t70) cc_final: 0.7927 (t0) REVERT: D 332 GLU cc_start: 0.6899 (pt0) cc_final: 0.6697 (pp20) REVERT: D 335 THR cc_start: 0.8977 (p) cc_final: 0.8347 (t) REVERT: D 346 GLN cc_start: 0.8972 (mt0) cc_final: 0.8688 (mt0) REVERT: D 488 MET cc_start: 0.8070 (ptp) cc_final: 0.7792 (ptp) REVERT: D 639 LEU cc_start: 0.8076 (tp) cc_final: 0.7554 (tp) REVERT: D 672 MET cc_start: 0.7978 (ttp) cc_final: 0.7775 (ttm) REVERT: D 706 MET cc_start: 0.8578 (tpp) cc_final: 0.8083 (tpp) REVERT: D 717 MET cc_start: 0.7767 (tpt) cc_final: 0.7500 (tpp) outliers start: 2 outliers final: 0 residues processed: 607 average time/residue: 0.2676 time to fit residues: 263.1486 Evaluate side-chains 484 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 3.9990 chunk 140 optimal weight: 0.0070 chunk 3 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 222 optimal weight: 0.0170 chunk 62 optimal weight: 0.8980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 695 GLN B 671 ASN B 695 GLN C 671 ASN C 695 GLN C 735 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21460 Z= 0.191 Angle : 0.699 8.119 29032 Z= 0.363 Chirality : 0.043 0.206 3308 Planarity : 0.005 0.059 3624 Dihedral : 6.418 48.403 2808 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.56 % Favored : 85.28 % Rotamer: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.97 (0.16), residues: 2568 helix: -0.82 (0.13), residues: 1388 sheet: -4.06 (0.38), residues: 72 loop : -3.41 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 493 HIS 0.004 0.001 HIS C 256 PHE 0.028 0.001 PHE C 261 TYR 0.018 0.002 TYR A 382 ARG 0.007 0.001 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 619 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8141 (mmt) cc_final: 0.7918 (mmm) REVERT: A 173 MET cc_start: 0.8621 (mtm) cc_final: 0.8152 (mtt) REVERT: A 198 ASP cc_start: 0.8122 (m-30) cc_final: 0.7166 (t70) REVERT: A 268 LEU cc_start: 0.9608 (tp) cc_final: 0.9383 (tp) REVERT: A 332 GLU cc_start: 0.7704 (pp20) cc_final: 0.7430 (pt0) REVERT: A 335 THR cc_start: 0.8945 (p) cc_final: 0.8268 (t) REVERT: A 346 GLN cc_start: 0.8841 (mt0) cc_final: 0.8570 (mt0) REVERT: A 371 ARG cc_start: 0.8484 (ptt90) cc_final: 0.8201 (ttp80) REVERT: A 488 MET cc_start: 0.8104 (ptp) cc_final: 0.7496 (ptp) REVERT: A 555 MET cc_start: 0.8734 (tmm) cc_final: 0.8486 (tmm) REVERT: A 631 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 639 LEU cc_start: 0.8076 (tp) cc_final: 0.7235 (tp) REVERT: B 159 MET cc_start: 0.8117 (mmt) cc_final: 0.7888 (mmm) REVERT: B 173 MET cc_start: 0.8631 (mtm) cc_final: 0.8138 (mtt) REVERT: B 198 ASP cc_start: 0.8124 (m-30) cc_final: 0.7161 (t70) REVERT: B 268 LEU cc_start: 0.9621 (tp) cc_final: 0.9386 (tp) REVERT: B 335 THR cc_start: 0.8932 (p) cc_final: 0.8277 (t) REVERT: B 346 GLN cc_start: 0.8815 (mt0) cc_final: 0.8588 (mt0) REVERT: B 488 MET cc_start: 0.8129 (ptp) cc_final: 0.7628 (ptp) REVERT: B 562 MET cc_start: 0.8841 (mmt) cc_final: 0.8394 (mmt) REVERT: B 639 LEU cc_start: 0.8037 (tp) cc_final: 0.7494 (tp) REVERT: B 706 MET cc_start: 0.8614 (tpp) cc_final: 0.7794 (tpp) REVERT: C 173 MET cc_start: 0.8582 (mtm) cc_final: 0.8090 (mtt) REVERT: C 198 ASP cc_start: 0.8159 (m-30) cc_final: 0.7175 (t70) REVERT: C 216 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7724 (tp40) REVERT: C 268 LEU cc_start: 0.9608 (tp) cc_final: 0.9355 (tp) REVERT: C 293 ASP cc_start: 0.8136 (t0) cc_final: 0.7494 (t0) REVERT: C 322 ASP cc_start: 0.8532 (t70) cc_final: 0.7923 (t0) REVERT: C 332 GLU cc_start: 0.6940 (pt0) cc_final: 0.6649 (pp20) REVERT: C 335 THR cc_start: 0.8918 (p) cc_final: 0.8282 (t) REVERT: C 346 GLN cc_start: 0.8855 (mt0) cc_final: 0.8605 (mt0) REVERT: C 371 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8218 (ttp80) REVERT: C 488 MET cc_start: 0.8147 (ptp) cc_final: 0.7694 (ptp) REVERT: C 562 MET cc_start: 0.8818 (mmt) cc_final: 0.8383 (mmt) REVERT: C 639 LEU cc_start: 0.8166 (tp) cc_final: 0.7790 (tp) REVERT: C 706 MET cc_start: 0.8611 (tpp) cc_final: 0.8075 (tpp) REVERT: D 171 CYS cc_start: 0.8731 (p) cc_final: 0.8514 (p) REVERT: D 173 MET cc_start: 0.8589 (mtm) cc_final: 0.8119 (mtt) REVERT: D 198 ASP cc_start: 0.8136 (m-30) cc_final: 0.7181 (t70) REVERT: D 216 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7917 (tp40) REVERT: D 268 LEU cc_start: 0.9590 (tp) cc_final: 0.9375 (tp) REVERT: D 293 ASP cc_start: 0.8610 (t0) cc_final: 0.8333 (t0) REVERT: D 322 ASP cc_start: 0.8507 (t70) cc_final: 0.7845 (t0) REVERT: D 335 THR cc_start: 0.8979 (p) cc_final: 0.8372 (t) REVERT: D 346 GLN cc_start: 0.8864 (mt0) cc_final: 0.8548 (mp10) REVERT: D 488 MET cc_start: 0.8092 (ptp) cc_final: 0.7481 (ptp) REVERT: D 562 MET cc_start: 0.8810 (mmt) cc_final: 0.8369 (mmt) REVERT: D 639 LEU cc_start: 0.7757 (tp) cc_final: 0.7436 (tp) REVERT: D 672 MET cc_start: 0.7908 (ttp) cc_final: 0.7596 (ttm) REVERT: D 706 MET cc_start: 0.8685 (tpp) cc_final: 0.8165 (tpp) REVERT: D 717 MET cc_start: 0.7392 (tpt) cc_final: 0.7141 (tpp) outliers start: 3 outliers final: 0 residues processed: 619 average time/residue: 0.2718 time to fit residues: 271.8658 Evaluate side-chains 493 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 0.0060 chunk 61 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 205 optimal weight: 0.0060 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.9816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21460 Z= 0.185 Angle : 0.685 8.226 29032 Z= 0.354 Chirality : 0.043 0.214 3308 Planarity : 0.005 0.058 3624 Dihedral : 6.188 48.173 2808 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.60 (0.16), residues: 2568 helix: -0.43 (0.14), residues: 1364 sheet: -3.72 (0.42), residues: 68 loop : -3.33 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 493 HIS 0.003 0.001 HIS D 745 PHE 0.022 0.001 PHE D 527 TYR 0.016 0.001 TYR A 594 ARG 0.005 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 609 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8750 (p) cc_final: 0.8546 (p) REVERT: A 173 MET cc_start: 0.8594 (mtm) cc_final: 0.8143 (mtt) REVERT: A 198 ASP cc_start: 0.8134 (m-30) cc_final: 0.7158 (t70) REVERT: A 268 LEU cc_start: 0.9585 (tp) cc_final: 0.9198 (tp) REVERT: A 335 THR cc_start: 0.8927 (p) cc_final: 0.8267 (t) REVERT: A 371 ARG cc_start: 0.8442 (ptt90) cc_final: 0.8201 (ttp80) REVERT: A 488 MET cc_start: 0.8124 (ptp) cc_final: 0.7672 (ptp) REVERT: A 562 MET cc_start: 0.8775 (mmt) cc_final: 0.8343 (mmt) REVERT: A 631 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 639 LEU cc_start: 0.8096 (tp) cc_final: 0.7223 (tp) REVERT: A 722 LYS cc_start: 0.6993 (tppp) cc_final: 0.6403 (tppp) REVERT: B 173 MET cc_start: 0.8609 (mtm) cc_final: 0.8143 (mtt) REVERT: B 198 ASP cc_start: 0.8133 (m-30) cc_final: 0.7161 (t70) REVERT: B 268 LEU cc_start: 0.9594 (tp) cc_final: 0.9161 (tp) REVERT: B 293 ASP cc_start: 0.8079 (t0) cc_final: 0.7790 (t0) REVERT: B 335 THR cc_start: 0.8899 (p) cc_final: 0.8250 (t) REVERT: B 346 GLN cc_start: 0.8770 (mt0) cc_final: 0.8517 (mt0) REVERT: B 371 ARG cc_start: 0.8563 (ptt90) cc_final: 0.8152 (ttp80) REVERT: B 393 THR cc_start: 0.8869 (p) cc_final: 0.8483 (p) REVERT: B 488 MET cc_start: 0.8144 (ptp) cc_final: 0.7684 (ptp) REVERT: B 562 MET cc_start: 0.8770 (mmt) cc_final: 0.8346 (mmt) REVERT: B 594 TYR cc_start: 0.9293 (t80) cc_final: 0.9046 (t80) REVERT: B 639 LEU cc_start: 0.8058 (tp) cc_final: 0.7525 (tp) REVERT: B 706 MET cc_start: 0.8567 (tpp) cc_final: 0.7835 (tpp) REVERT: C 173 MET cc_start: 0.8502 (mtm) cc_final: 0.8072 (mtt) REVERT: C 198 ASP cc_start: 0.8157 (m-30) cc_final: 0.7156 (t70) REVERT: C 268 LEU cc_start: 0.9586 (tp) cc_final: 0.9146 (tp) REVERT: C 322 ASP cc_start: 0.8410 (t70) cc_final: 0.8146 (t0) REVERT: C 332 GLU cc_start: 0.7139 (pt0) cc_final: 0.6729 (pp20) REVERT: C 335 THR cc_start: 0.8919 (p) cc_final: 0.8302 (t) REVERT: C 346 GLN cc_start: 0.8805 (mt0) cc_final: 0.8509 (mp10) REVERT: C 371 ARG cc_start: 0.8403 (ptt90) cc_final: 0.8158 (ttp80) REVERT: C 488 MET cc_start: 0.8148 (ptp) cc_final: 0.7701 (ptp) REVERT: C 562 MET cc_start: 0.8775 (mmt) cc_final: 0.8379 (mmt) REVERT: C 639 LEU cc_start: 0.8213 (tp) cc_final: 0.7864 (tp) REVERT: C 706 MET cc_start: 0.8575 (tpp) cc_final: 0.8132 (tpp) REVERT: D 173 MET cc_start: 0.8569 (mtm) cc_final: 0.8136 (mtt) REVERT: D 198 ASP cc_start: 0.8155 (m-30) cc_final: 0.7142 (t70) REVERT: D 268 LEU cc_start: 0.9586 (tp) cc_final: 0.9192 (tp) REVERT: D 293 ASP cc_start: 0.8044 (t0) cc_final: 0.7693 (t0) REVERT: D 322 ASP cc_start: 0.8438 (t70) cc_final: 0.7974 (t0) REVERT: D 335 THR cc_start: 0.9057 (p) cc_final: 0.8408 (t) REVERT: D 346 GLN cc_start: 0.8780 (mt0) cc_final: 0.8495 (mp10) REVERT: D 359 TYR cc_start: 0.8955 (t80) cc_final: 0.8713 (t80) REVERT: D 488 MET cc_start: 0.8112 (ptp) cc_final: 0.7587 (ptp) REVERT: D 562 MET cc_start: 0.8778 (mmt) cc_final: 0.8381 (mmt) REVERT: D 639 LEU cc_start: 0.7759 (tp) cc_final: 0.7457 (tp) REVERT: D 672 MET cc_start: 0.7743 (ttp) cc_final: 0.7485 (tmm) REVERT: D 706 MET cc_start: 0.8680 (tpp) cc_final: 0.8208 (tpp) REVERT: D 717 MET cc_start: 0.7350 (tpt) cc_final: 0.7012 (tpp) REVERT: D 722 LYS cc_start: 0.7180 (tppp) cc_final: 0.6630 (tppp) outliers start: 3 outliers final: 0 residues processed: 609 average time/residue: 0.2692 time to fit residues: 265.1556 Evaluate side-chains 491 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21460 Z= 0.257 Angle : 0.722 8.837 29032 Z= 0.371 Chirality : 0.045 0.273 3308 Planarity : 0.005 0.072 3624 Dihedral : 6.196 48.360 2808 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.26 % Favored : 84.58 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.49 (0.16), residues: 2568 helix: -0.30 (0.14), residues: 1364 sheet: -4.02 (0.44), residues: 68 loop : -3.31 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 481 HIS 0.003 0.001 HIS A 430 PHE 0.041 0.002 PHE D 261 TYR 0.015 0.002 TYR D 208 ARG 0.008 0.001 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 609 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8625 (mtm) cc_final: 0.8175 (mtt) REVERT: A 198 ASP cc_start: 0.8163 (m-30) cc_final: 0.7178 (t70) REVERT: A 216 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7857 (tp40) REVERT: A 268 LEU cc_start: 0.9581 (tp) cc_final: 0.9358 (tp) REVERT: A 332 GLU cc_start: 0.7763 (pp20) cc_final: 0.7556 (pt0) REVERT: A 335 THR cc_start: 0.8952 (p) cc_final: 0.8252 (t) REVERT: A 488 MET cc_start: 0.8183 (ptp) cc_final: 0.7762 (ptp) REVERT: A 562 MET cc_start: 0.8805 (mmt) cc_final: 0.8362 (mmt) REVERT: A 637 ILE cc_start: 0.8739 (mp) cc_final: 0.8251 (mm) REVERT: A 639 LEU cc_start: 0.8248 (tp) cc_final: 0.7765 (tp) REVERT: A 717 MET cc_start: 0.6237 (ttt) cc_final: 0.5783 (tpp) REVERT: B 173 MET cc_start: 0.8628 (mtm) cc_final: 0.8166 (mtt) REVERT: B 198 ASP cc_start: 0.8153 (m-30) cc_final: 0.7165 (t70) REVERT: B 268 LEU cc_start: 0.9565 (tp) cc_final: 0.9356 (tp) REVERT: B 335 THR cc_start: 0.8903 (p) cc_final: 0.8241 (t) REVERT: B 346 GLN cc_start: 0.8865 (mt0) cc_final: 0.8639 (mt0) REVERT: B 488 MET cc_start: 0.8203 (ptp) cc_final: 0.7759 (ptp) REVERT: B 562 MET cc_start: 0.8814 (mmt) cc_final: 0.8369 (mmt) REVERT: B 639 LEU cc_start: 0.8233 (tp) cc_final: 0.7777 (tp) REVERT: B 706 MET cc_start: 0.8715 (tpp) cc_final: 0.8033 (tpp) REVERT: C 159 MET cc_start: 0.8199 (mtt) cc_final: 0.7901 (mtt) REVERT: C 173 MET cc_start: 0.8593 (mtm) cc_final: 0.8159 (mtt) REVERT: C 198 ASP cc_start: 0.8167 (m-30) cc_final: 0.7217 (t70) REVERT: C 335 THR cc_start: 0.8923 (p) cc_final: 0.8324 (t) REVERT: C 346 GLN cc_start: 0.8870 (mt0) cc_final: 0.8645 (mt0) REVERT: C 488 MET cc_start: 0.8201 (ptp) cc_final: 0.7773 (ptp) REVERT: C 562 MET cc_start: 0.8779 (mmt) cc_final: 0.8360 (mmt) REVERT: C 639 LEU cc_start: 0.8268 (tp) cc_final: 0.7895 (tp) REVERT: C 706 MET cc_start: 0.8699 (tpp) cc_final: 0.8290 (tpp) REVERT: D 159 MET cc_start: 0.8143 (mtt) cc_final: 0.7586 (mtt) REVERT: D 173 MET cc_start: 0.8586 (mtm) cc_final: 0.8187 (mtt) REVERT: D 198 ASP cc_start: 0.8131 (m-30) cc_final: 0.7147 (t70) REVERT: D 202 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8431 (ttt90) REVERT: D 335 THR cc_start: 0.9034 (p) cc_final: 0.8396 (t) REVERT: D 346 GLN cc_start: 0.8864 (mt0) cc_final: 0.8623 (mt0) REVERT: D 488 MET cc_start: 0.8182 (ptp) cc_final: 0.7657 (ptp) REVERT: D 562 MET cc_start: 0.8798 (mmt) cc_final: 0.8382 (mmt) REVERT: D 639 LEU cc_start: 0.7881 (tp) cc_final: 0.7551 (tp) REVERT: D 672 MET cc_start: 0.7990 (ttp) cc_final: 0.7786 (ttm) REVERT: D 706 MET cc_start: 0.8726 (tpp) cc_final: 0.8323 (tpp) REVERT: D 717 MET cc_start: 0.7523 (tpt) cc_final: 0.7238 (tpp) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.2832 time to fit residues: 276.5169 Evaluate side-chains 478 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 193 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 585 HIS A 671 ASN B 514 GLN B 585 HIS B 671 ASN C 514 GLN C 585 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21460 Z= 0.181 Angle : 0.706 8.457 29032 Z= 0.358 Chirality : 0.043 0.244 3308 Planarity : 0.005 0.061 3624 Dihedral : 6.022 48.456 2808 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.24 % Favored : 86.60 % Rotamer: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.29 (0.16), residues: 2568 helix: -0.13 (0.14), residues: 1416 sheet: -3.29 (0.61), residues: 44 loop : -3.43 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 481 HIS 0.006 0.001 HIS C 244 PHE 0.025 0.001 PHE D 527 TYR 0.016 0.001 TYR A 359 ARG 0.008 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 626 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8579 (mtm) cc_final: 0.8199 (mtt) REVERT: A 198 ASP cc_start: 0.8146 (m-30) cc_final: 0.7031 (t0) REVERT: A 268 LEU cc_start: 0.9606 (tp) cc_final: 0.9281 (tp) REVERT: A 335 THR cc_start: 0.8889 (p) cc_final: 0.8241 (t) REVERT: A 359 TYR cc_start: 0.8977 (t80) cc_final: 0.8627 (t80) REVERT: A 488 MET cc_start: 0.8154 (ptp) cc_final: 0.7706 (ptp) REVERT: A 562 MET cc_start: 0.8800 (mmt) cc_final: 0.8396 (mmt) REVERT: A 639 LEU cc_start: 0.8085 (tp) cc_final: 0.7608 (tp) REVERT: A 706 MET cc_start: 0.8338 (tpp) cc_final: 0.7984 (tpp) REVERT: A 717 MET cc_start: 0.5621 (ttt) cc_final: 0.5403 (tpp) REVERT: B 173 MET cc_start: 0.8579 (mtm) cc_final: 0.8171 (mtt) REVERT: B 198 ASP cc_start: 0.8129 (m-30) cc_final: 0.7093 (t70) REVERT: B 248 VAL cc_start: 0.9284 (m) cc_final: 0.8975 (p) REVERT: B 268 LEU cc_start: 0.9572 (tp) cc_final: 0.9155 (tp) REVERT: B 322 ASP cc_start: 0.8467 (t70) cc_final: 0.7943 (t0) REVERT: B 335 THR cc_start: 0.8842 (p) cc_final: 0.8217 (t) REVERT: B 346 GLN cc_start: 0.8733 (mt0) cc_final: 0.8447 (mt0) REVERT: B 488 MET cc_start: 0.8180 (ptp) cc_final: 0.7716 (ptp) REVERT: B 562 MET cc_start: 0.8768 (mmt) cc_final: 0.8415 (mmt) REVERT: B 639 LEU cc_start: 0.8050 (tp) cc_final: 0.7610 (tp) REVERT: B 706 MET cc_start: 0.8623 (tpp) cc_final: 0.7937 (tpp) REVERT: C 173 MET cc_start: 0.8490 (mtm) cc_final: 0.8117 (mtt) REVERT: C 198 ASP cc_start: 0.8377 (m-30) cc_final: 0.7189 (t70) REVERT: C 268 LEU cc_start: 0.9531 (tp) cc_final: 0.8933 (tp) REVERT: C 335 THR cc_start: 0.8867 (p) cc_final: 0.8306 (t) REVERT: C 346 GLN cc_start: 0.8734 (mt0) cc_final: 0.8443 (mt0) REVERT: C 488 MET cc_start: 0.8177 (ptp) cc_final: 0.7741 (ptp) REVERT: C 562 MET cc_start: 0.8712 (mmt) cc_final: 0.8336 (mmt) REVERT: C 639 LEU cc_start: 0.8233 (tp) cc_final: 0.7899 (tp) REVERT: C 706 MET cc_start: 0.8631 (tpp) cc_final: 0.7905 (tpp) REVERT: C 717 MET cc_start: 0.6046 (tpt) cc_final: 0.5806 (tpp) REVERT: D 134 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 138 LEU cc_start: 0.8870 (mt) cc_final: 0.8433 (mt) REVERT: D 159 MET cc_start: 0.8069 (mtt) cc_final: 0.7509 (mtt) REVERT: D 173 MET cc_start: 0.8505 (mtm) cc_final: 0.8121 (mtt) REVERT: D 198 ASP cc_start: 0.8096 (m-30) cc_final: 0.7093 (t70) REVERT: D 202 ARG cc_start: 0.8636 (ttt180) cc_final: 0.8429 (ttt90) REVERT: D 248 VAL cc_start: 0.9293 (m) cc_final: 0.8930 (p) REVERT: D 251 ASN cc_start: 0.8222 (t0) cc_final: 0.7700 (t0) REVERT: D 268 LEU cc_start: 0.9538 (tp) cc_final: 0.9295 (tp) REVERT: D 335 THR cc_start: 0.8922 (p) cc_final: 0.8293 (t) REVERT: D 346 GLN cc_start: 0.8774 (mt0) cc_final: 0.8467 (mt0) REVERT: D 393 THR cc_start: 0.8907 (p) cc_final: 0.8578 (m) REVERT: D 488 MET cc_start: 0.8151 (ptp) cc_final: 0.7739 (ptp) REVERT: D 562 MET cc_start: 0.8767 (mmt) cc_final: 0.8374 (mmt) REVERT: D 630 LEU cc_start: 0.9183 (mt) cc_final: 0.8920 (mm) REVERT: D 639 LEU cc_start: 0.7753 (tp) cc_final: 0.7443 (tp) REVERT: D 672 MET cc_start: 0.7811 (ttp) cc_final: 0.7569 (ttm) REVERT: D 706 MET cc_start: 0.8661 (tpp) cc_final: 0.7953 (tpp) outliers start: 2 outliers final: 0 residues processed: 626 average time/residue: 0.2670 time to fit residues: 269.1929 Evaluate side-chains 513 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 180 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 671 ASN B 244 HIS B 273 ASN B 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21460 Z= 0.187 Angle : 0.705 8.521 29032 Z= 0.360 Chirality : 0.044 0.252 3308 Planarity : 0.005 0.061 3624 Dihedral : 5.987 48.144 2808 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer: Outliers : 0.13 % Allowed : 0.74 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.25 (0.16), residues: 2568 helix: -0.08 (0.14), residues: 1416 sheet: -3.62 (0.50), residues: 64 loop : -3.40 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 742 HIS 0.005 0.001 HIS A 745 PHE 0.030 0.001 PHE C 261 TYR 0.021 0.002 TYR C 382 ARG 0.005 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 616 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 138 LEU cc_start: 0.8875 (mt) cc_final: 0.8433 (mt) REVERT: A 173 MET cc_start: 0.8605 (mtm) cc_final: 0.8176 (mtt) REVERT: A 198 ASP cc_start: 0.8339 (m-30) cc_final: 0.7165 (t70) REVERT: A 248 VAL cc_start: 0.9290 (m) cc_final: 0.9022 (p) REVERT: A 322 ASP cc_start: 0.8432 (t0) cc_final: 0.8098 (t70) REVERT: A 335 THR cc_start: 0.8920 (p) cc_final: 0.8283 (t) REVERT: A 488 MET cc_start: 0.8177 (ptp) cc_final: 0.7594 (ptp) REVERT: A 562 MET cc_start: 0.8783 (mmt) cc_final: 0.8429 (mmt) REVERT: A 639 LEU cc_start: 0.8137 (tp) cc_final: 0.7739 (tp) REVERT: A 706 MET cc_start: 0.8369 (tpp) cc_final: 0.8042 (tpp) REVERT: B 134 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7761 (tm-30) REVERT: B 138 LEU cc_start: 0.8861 (mt) cc_final: 0.8426 (mt) REVERT: B 173 MET cc_start: 0.8554 (mtm) cc_final: 0.8077 (mtt) REVERT: B 198 ASP cc_start: 0.8334 (m-30) cc_final: 0.7163 (t70) REVERT: B 248 VAL cc_start: 0.9302 (m) cc_final: 0.8984 (p) REVERT: B 268 LEU cc_start: 0.9554 (tp) cc_final: 0.9294 (tp) REVERT: B 322 ASP cc_start: 0.8252 (t70) cc_final: 0.8004 (t0) REVERT: B 335 THR cc_start: 0.8842 (p) cc_final: 0.8241 (t) REVERT: B 346 GLN cc_start: 0.8750 (mt0) cc_final: 0.8487 (mt0) REVERT: B 396 ASP cc_start: 0.8241 (t0) cc_final: 0.7905 (t70) REVERT: B 488 MET cc_start: 0.8190 (ptp) cc_final: 0.7737 (ptp) REVERT: B 562 MET cc_start: 0.8814 (mmt) cc_final: 0.8403 (mmt) REVERT: B 639 LEU cc_start: 0.8106 (tp) cc_final: 0.7696 (tp) REVERT: B 706 MET cc_start: 0.8625 (tpp) cc_final: 0.7956 (tpp) REVERT: B 717 MET cc_start: 0.6058 (tpt) cc_final: 0.5777 (tpp) REVERT: C 134 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 138 LEU cc_start: 0.8848 (mt) cc_final: 0.8432 (mt) REVERT: C 155 PRO cc_start: 0.8666 (Cg_endo) cc_final: 0.8465 (Cg_exo) REVERT: C 173 MET cc_start: 0.8550 (mtm) cc_final: 0.8184 (mtt) REVERT: C 198 ASP cc_start: 0.8402 (m-30) cc_final: 0.7201 (t0) REVERT: C 248 VAL cc_start: 0.9316 (m) cc_final: 0.9018 (p) REVERT: C 268 LEU cc_start: 0.9556 (tp) cc_final: 0.9129 (tp) REVERT: C 335 THR cc_start: 0.8875 (p) cc_final: 0.8318 (t) REVERT: C 346 GLN cc_start: 0.8738 (mt0) cc_final: 0.8483 (mt0) REVERT: C 359 TYR cc_start: 0.8840 (t80) cc_final: 0.8304 (t80) REVERT: C 488 MET cc_start: 0.8185 (ptp) cc_final: 0.7764 (ptp) REVERT: C 562 MET cc_start: 0.8720 (mmt) cc_final: 0.8377 (mmt) REVERT: C 639 LEU cc_start: 0.8273 (tp) cc_final: 0.7889 (tp) REVERT: C 706 MET cc_start: 0.8622 (tpp) cc_final: 0.7928 (tpp) REVERT: C 717 MET cc_start: 0.6085 (tpt) cc_final: 0.5851 (tpp) REVERT: D 134 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7745 (tm-30) REVERT: D 138 LEU cc_start: 0.8853 (mt) cc_final: 0.8429 (mt) REVERT: D 159 MET cc_start: 0.8059 (mtt) cc_final: 0.7504 (mtt) REVERT: D 173 MET cc_start: 0.8560 (mtm) cc_final: 0.8182 (mtt) REVERT: D 198 ASP cc_start: 0.8140 (m-30) cc_final: 0.7111 (t70) REVERT: D 202 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8391 (ttt90) REVERT: D 248 VAL cc_start: 0.9274 (m) cc_final: 0.8916 (p) REVERT: D 251 ASN cc_start: 0.8049 (t0) cc_final: 0.7598 (t0) REVERT: D 335 THR cc_start: 0.8943 (p) cc_final: 0.8311 (t) REVERT: D 346 GLN cc_start: 0.8783 (mt0) cc_final: 0.8469 (mt0) REVERT: D 359 TYR cc_start: 0.8911 (t80) cc_final: 0.8516 (t80) REVERT: D 485 LEU cc_start: 0.8507 (tt) cc_final: 0.8261 (tp) REVERT: D 488 MET cc_start: 0.8171 (ptp) cc_final: 0.7750 (ptp) REVERT: D 562 MET cc_start: 0.8769 (mmt) cc_final: 0.8412 (mmt) REVERT: D 706 MET cc_start: 0.8671 (tpp) cc_final: 0.7969 (tpp) outliers start: 3 outliers final: 0 residues processed: 616 average time/residue: 0.2688 time to fit residues: 269.5206 Evaluate side-chains 504 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 671 ASN B 273 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 683 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN D 182 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21460 Z= 0.222 Angle : 0.718 8.311 29032 Z= 0.368 Chirality : 0.044 0.252 3308 Planarity : 0.005 0.063 3624 Dihedral : 5.933 47.373 2808 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.75 % Favored : 86.06 % Rotamer: Outliers : 0.09 % Allowed : 0.30 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.18 (0.16), residues: 2568 helix: -0.10 (0.14), residues: 1436 sheet: -3.64 (0.51), residues: 68 loop : -3.29 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 742 HIS 0.004 0.001 HIS B 745 PHE 0.025 0.001 PHE D 527 TYR 0.029 0.001 TYR D 594 ARG 0.006 0.000 ARG D 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 588 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 138 LEU cc_start: 0.8885 (mt) cc_final: 0.8454 (mt) REVERT: A 171 CYS cc_start: 0.8769 (p) cc_final: 0.8566 (p) REVERT: A 173 MET cc_start: 0.8581 (mtm) cc_final: 0.8170 (mtt) REVERT: A 198 ASP cc_start: 0.8455 (m-30) cc_final: 0.7165 (t0) REVERT: A 248 VAL cc_start: 0.9261 (m) cc_final: 0.9034 (p) REVERT: A 268 LEU cc_start: 0.9540 (tp) cc_final: 0.9019 (tp) REVERT: A 322 ASP cc_start: 0.8458 (t0) cc_final: 0.8186 (t70) REVERT: A 335 THR cc_start: 0.8884 (p) cc_final: 0.8263 (t) REVERT: A 488 MET cc_start: 0.8186 (ptp) cc_final: 0.7579 (ptp) REVERT: A 562 MET cc_start: 0.8788 (mmt) cc_final: 0.8353 (mmt) REVERT: A 639 LEU cc_start: 0.8199 (tp) cc_final: 0.7733 (tp) REVERT: A 706 MET cc_start: 0.8411 (tpp) cc_final: 0.8074 (tpp) REVERT: B 155 PRO cc_start: 0.8655 (Cg_endo) cc_final: 0.8433 (Cg_exo) REVERT: B 173 MET cc_start: 0.8569 (mtm) cc_final: 0.8133 (mtt) REVERT: B 198 ASP cc_start: 0.8421 (m-30) cc_final: 0.7124 (t0) REVERT: B 248 VAL cc_start: 0.9305 (m) cc_final: 0.9047 (p) REVERT: B 322 ASP cc_start: 0.8354 (t70) cc_final: 0.7767 (t0) REVERT: B 335 THR cc_start: 0.8813 (p) cc_final: 0.8208 (t) REVERT: B 396 ASP cc_start: 0.8179 (t0) cc_final: 0.7815 (t70) REVERT: B 488 MET cc_start: 0.8194 (ptp) cc_final: 0.7741 (ptp) REVERT: B 639 LEU cc_start: 0.8176 (tp) cc_final: 0.7705 (tp) REVERT: B 706 MET cc_start: 0.8629 (tpp) cc_final: 0.7961 (tpp) REVERT: C 173 MET cc_start: 0.8504 (mtm) cc_final: 0.8065 (mtt) REVERT: C 198 ASP cc_start: 0.8416 (m-30) cc_final: 0.7156 (t0) REVERT: C 248 VAL cc_start: 0.9349 (m) cc_final: 0.9080 (p) REVERT: C 322 ASP cc_start: 0.8393 (t70) cc_final: 0.8037 (t70) REVERT: C 335 THR cc_start: 0.8889 (p) cc_final: 0.8307 (t) REVERT: C 359 TYR cc_start: 0.8969 (t80) cc_final: 0.8506 (t80) REVERT: C 488 MET cc_start: 0.8208 (ptp) cc_final: 0.7778 (ptp) REVERT: C 562 MET cc_start: 0.8761 (mmt) cc_final: 0.8347 (mmt) REVERT: C 639 LEU cc_start: 0.8234 (tp) cc_final: 0.7859 (tp) REVERT: C 706 MET cc_start: 0.8680 (tpp) cc_final: 0.8001 (tpp) REVERT: C 717 MET cc_start: 0.6250 (tpt) cc_final: 0.6006 (tpp) REVERT: D 159 MET cc_start: 0.8174 (mtt) cc_final: 0.7619 (mtt) REVERT: D 173 MET cc_start: 0.8561 (mtm) cc_final: 0.8152 (mtt) REVERT: D 198 ASP cc_start: 0.8111 (m-30) cc_final: 0.7113 (t70) REVERT: D 202 ARG cc_start: 0.8612 (ttt180) cc_final: 0.8403 (ttt90) REVERT: D 248 VAL cc_start: 0.9319 (m) cc_final: 0.9030 (p) REVERT: D 251 ASN cc_start: 0.8167 (t0) cc_final: 0.7610 (t0) REVERT: D 322 ASP cc_start: 0.8431 (t70) cc_final: 0.7860 (t70) REVERT: D 335 THR cc_start: 0.8906 (p) cc_final: 0.8300 (t) REVERT: D 488 MET cc_start: 0.8184 (ptp) cc_final: 0.7649 (ptp) REVERT: D 562 MET cc_start: 0.8771 (mmt) cc_final: 0.8427 (mmt) REVERT: D 706 MET cc_start: 0.8761 (tpp) cc_final: 0.8055 (tpp) REVERT: D 722 LYS cc_start: 0.7014 (tppp) cc_final: 0.6330 (tppp) outliers start: 2 outliers final: 0 residues processed: 588 average time/residue: 0.2677 time to fit residues: 256.3212 Evaluate side-chains 490 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 244 HIS B 412 ASN B 561 ASN B 671 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 683 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 671 ASN D 683 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111199 restraints weight = 44490.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114084 restraints weight = 27700.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116123 restraints weight = 19724.381| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21460 Z= 0.187 Angle : 0.704 9.070 29032 Z= 0.357 Chirality : 0.043 0.245 3308 Planarity : 0.005 0.053 3624 Dihedral : 5.836 47.245 2808 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.51 % Favored : 86.33 % Rotamer: Outliers : 0.09 % Allowed : 0.78 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.00 (0.17), residues: 2568 helix: 0.00 (0.14), residues: 1428 sheet: -3.59 (0.50), residues: 68 loop : -3.11 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 742 HIS 0.006 0.001 HIS A 745 PHE 0.027 0.001 PHE B 527 TYR 0.020 0.001 TYR C 594 ARG 0.006 0.000 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5119.96 seconds wall clock time: 94 minutes 27.36 seconds (5667.36 seconds total)