Starting phenix.real_space_refine on Sun Aug 24 15:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_8919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_8919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_8919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_8919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dvw_8919/08_2025/6dvw_8919.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D Time building chain proxies: 4.20, per 1000 atoms: 0.20 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: 1.38 Conformation dependent library (CDL) restraints added in 824.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 3.14 Time building geometry restraints manager: 1.89 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: 0.06 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: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.290 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- 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= 0.381 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.014 0.002 ARG D 226 TYR 0.019 0.003 TYR D 439 PHE 0.024 0.003 PHE D 656 TRP 0.021 0.003 TRP A 380 HIS 0.009 0.002 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00834 (21460) covalent geometry : angle 1.19084 (29032) hydrogen bonds : bond 0.30907 ( 790) hydrogen bonds : angle 9.25384 ( 2292) *********************** 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 to be fit. rotamer outliers: 20 poor density : 765 time to evaluate : 0.744 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: 0.8160 (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: 0.7150 (t70) REVERT: A 216 GLN cc_start: 0.8519 (tp-100) cc_final: 0.7531 (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: 0.7795 (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: 0.8415 (t) REVERT: A 346 GLN cc_start: 0.9022 (mt0) cc_final: 0.8581 (mt0) REVERT: A 439 TYR cc_start: 0.8320 (m-80) cc_final: 0.8079 (m-80) REVERT: A 446 CYS cc_start: 0.8737 (m) cc_final: 0.8159 (t) REVERT: A 453 ILE cc_start: 0.9527 (mt) cc_final: 0.9324 (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: 0.8445 (p0) REVERT: A 639 LEU cc_start: 0.8262 (tp) cc_final: 0.7725 (tp) REVERT: A 672 MET cc_start: 0.7937 (ttp) cc_final: 0.7725 (tmm) REVERT: A 696 ARG cc_start: 0.8950 (ttm170) cc_final: 0.8521 (ttm170) REVERT: A 705 LYS cc_start: 0.9089 (mttt) cc_final: 0.8828 (mttp) REVERT: A 706 MET cc_start: 0.8006 (tmm) cc_final: 0.7174 (tmm) REVERT: A 707 LEU cc_start: 0.6159 (mt) cc_final: 0.5214 (mt) REVERT: B 141 ASP cc_start: 0.8550 (m-30) cc_final: 0.8157 (p0) REVERT: B 173 MET cc_start: 0.8572 (mtm) cc_final: 0.8020 (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: 0.7531 (tp40) REVERT: B 220 ASN cc_start: 0.9124 (m-40) cc_final: 0.8805 (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: 0.7837 (t0) REVERT: B 268 LEU cc_start: 0.9429 (tp) cc_final: 0.9048 (tp) REVERT: B 335 THR cc_start: 0.9106 (p) cc_final: 0.8443 (t) REVERT: B 346 GLN cc_start: 0.9037 (mt0) cc_final: 0.8622 (mt0) REVERT: B 439 TYR cc_start: 0.8390 (m-80) cc_final: 0.8162 (m-80) REVERT: B 446 CYS cc_start: 0.8814 (m) cc_final: 0.8198 (t) REVERT: B 603 VAL cc_start: 0.9273 (t) cc_final: 0.8833 (p) REVERT: B 639 LEU cc_start: 0.8236 (tp) cc_final: 0.7714 (tp) REVERT: B 696 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8535 (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: 0.7135 (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: 0.7986 (mtt) REVERT: C 198 ASP cc_start: 0.7976 (m-30) cc_final: 0.7133 (t70) REVERT: C 216 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7531 (tp40) REVERT: C 220 ASN cc_start: 0.9147 (m-40) cc_final: 0.8829 (m-40) REVERT: C 221 ILE cc_start: 0.9701 (tp) cc_final: 0.9439 (tp) REVERT: C 223 ILE cc_start: 0.9714 (mt) cc_final: 0.9509 (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: 0.9010 (tp) REVERT: C 335 THR cc_start: 0.9136 (p) cc_final: 0.8488 (t) REVERT: C 346 GLN cc_start: 0.9042 (mt0) cc_final: 0.8614 (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: 0.8177 (t) REVERT: C 603 VAL cc_start: 0.9285 (t) cc_final: 0.8973 (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: 0.7777 (tp) REVERT: C 705 LYS cc_start: 0.9090 (mttt) cc_final: 0.8826 (mttp) REVERT: C 706 MET cc_start: 0.7989 (tmm) cc_final: 0.7137 (tmm) REVERT: C 707 LEU cc_start: 0.6140 (mt) cc_final: 0.5190 (mt) REVERT: C 717 MET cc_start: 0.8103 (tpt) cc_final: 0.7877 (tpp) REVERT: D 141 ASP cc_start: 0.8589 (m-30) cc_final: 0.8183 (p0) REVERT: D 173 MET cc_start: 0.8595 (mtm) cc_final: 0.8116 (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: 0.9140 (mt) REVERT: D 216 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7557 (tp40) REVERT: D 220 ASN cc_start: 0.9163 (m-40) cc_final: 0.8783 (m-40) REVERT: D 221 ILE cc_start: 0.9702 (tp) cc_final: 0.9434 (tp) REVERT: D 251 ASN cc_start: 0.8245 (t0) cc_final: 0.7741 (t0) REVERT: D 268 LEU cc_start: 0.9388 (tp) cc_final: 0.9044 (tp) REVERT: D 335 THR cc_start: 0.9151 (p) cc_final: 0.8476 (t) REVERT: D 346 GLN cc_start: 0.9022 (mt0) cc_final: 0.8605 (mt0) REVERT: D 392 LEU cc_start: 0.8460 (tp) cc_final: 0.8243 (tp) REVERT: D 446 CYS cc_start: 0.8755 (m) cc_final: 0.8168 (t) REVERT: D 639 LEU cc_start: 0.8334 (tp) cc_final: 0.7805 (tp) REVERT: D 672 MET cc_start: 0.8002 (ttp) cc_final: 0.7672 (ttp) REVERT: D 705 LYS cc_start: 0.9089 (mttt) cc_final: 0.8825 (mttp) REVERT: D 706 MET cc_start: 0.8000 (tmm) cc_final: 0.7150 (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: 0.7857 (tpp) outliers start: 20 outliers final: 8 residues processed: 773 average time/residue: 0.1193 time to fit residues: 146.1993 Evaluate side-chains 508 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 500 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 C 251 ASN C 643 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107028 restraints weight = 44780.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109831 restraints weight = 27401.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111682 restraints weight = 19397.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113101 restraints weight = 15260.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113959 restraints weight = 12880.392| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21460 Z= 0.173 Angle : 0.795 8.674 29032 Z= 0.419 Chirality : 0.044 0.229 3308 Planarity : 0.006 0.072 3624 Dihedral : 7.329 49.504 2808 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.05 % Favored : 86.80 % Rotamer: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.52 (0.14), residues: 2568 helix: -2.46 (0.11), residues: 1412 sheet: -4.69 (0.32), residues: 76 loop : -3.56 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 733 TYR 0.011 0.001 TYR D 213 PHE 0.015 0.001 PHE C 261 TRP 0.014 0.002 TRP C 739 HIS 0.002 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00355 (21460) covalent geometry : angle 0.79536 (29032) hydrogen bonds : bond 0.06388 ( 790) hydrogen bonds : angle 5.06227 ( 2292) *********************** 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 712 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 708 time to evaluate : 0.873 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: A 173 MET cc_start: 0.8834 (mtm) cc_final: 0.8327 (mtt) REVERT: A 198 ASP cc_start: 0.8066 (m-30) cc_final: 0.7136 (t70) REVERT: A 216 GLN cc_start: 0.8566 (tp-100) cc_final: 0.7914 (tp40) REVERT: A 251 ASN cc_start: 0.7946 (t0) cc_final: 0.7689 (t0) REVERT: A 257 GLU cc_start: 0.7756 (pt0) cc_final: 0.7446 (pt0) REVERT: A 306 VAL cc_start: 0.9096 (t) cc_final: 0.8881 (t) REVERT: A 332 GLU cc_start: 0.6974 (pt0) cc_final: 0.6696 (pp20) REVERT: A 335 THR cc_start: 0.9047 (p) cc_final: 0.8449 (t) REVERT: A 346 GLN cc_start: 0.9071 (mt0) cc_final: 0.8768 (mt0) REVERT: A 446 CYS cc_start: 0.8780 (m) cc_final: 0.8475 (t) REVERT: A 592 PHE cc_start: 0.8281 (t80) cc_final: 0.8059 (t80) REVERT: A 695 GLN cc_start: 0.8550 (mt0) cc_final: 0.8228 (mt0) REVERT: A 696 ARG cc_start: 0.9088 (ttm170) cc_final: 0.8625 (ttm170) REVERT: A 704 GLU cc_start: 0.6896 (tp30) cc_final: 0.6683 (tp30) REVERT: A 722 LYS cc_start: 0.7286 (tptp) cc_final: 0.7063 (tptp) REVERT: A 740 THR cc_start: 0.6733 (m) cc_final: 0.6399 (m) REVERT: B 173 MET cc_start: 0.8821 (mtm) cc_final: 0.8306 (mtt) REVERT: B 198 ASP cc_start: 0.8053 (m-30) cc_final: 0.7122 (t70) REVERT: B 216 GLN cc_start: 0.8574 (tp-100) cc_final: 0.7921 (tp40) REVERT: B 251 ASN cc_start: 0.7940 (t0) cc_final: 0.7668 (t0) REVERT: B 257 GLU cc_start: 0.7758 (pt0) cc_final: 0.7447 (pt0) REVERT: B 306 VAL cc_start: 0.9084 (t) cc_final: 0.8875 (t) REVERT: B 332 GLU cc_start: 0.6997 (pt0) cc_final: 0.6653 (pp20) REVERT: B 335 THR cc_start: 0.9047 (p) cc_final: 0.8440 (t) REVERT: B 346 GLN cc_start: 0.9035 (mt0) cc_final: 0.8732 (mt0) REVERT: B 446 CYS cc_start: 0.8770 (m) cc_final: 0.8486 (t) REVERT: B 695 GLN cc_start: 0.8551 (mt0) cc_final: 0.8201 (mt0) REVERT: B 722 LYS cc_start: 0.7283 (tptp) cc_final: 0.6969 (tptp) REVERT: B 740 THR cc_start: 0.6757 (m) cc_final: 0.6422 (m) REVERT: C 173 MET cc_start: 0.8799 (mtm) cc_final: 0.8265 (mtt) REVERT: C 198 ASP cc_start: 0.8089 (m-30) cc_final: 0.7143 (t70) REVERT: C 216 GLN cc_start: 0.8555 (tp-100) cc_final: 0.7921 (tp40) REVERT: C 251 ASN cc_start: 0.7937 (t0) cc_final: 0.7673 (t0) REVERT: C 257 GLU cc_start: 0.7750 (pt0) cc_final: 0.7456 (pt0) REVERT: C 332 GLU cc_start: 0.7050 (pt0) cc_final: 0.6722 (pp20) REVERT: C 335 THR cc_start: 0.9038 (p) cc_final: 0.8432 (t) REVERT: C 346 GLN cc_start: 0.9052 (mt0) cc_final: 0.8676 (mt0) REVERT: C 446 CYS cc_start: 0.8811 (m) cc_final: 0.8501 (t) REVERT: C 521 TRP cc_start: 0.8385 (m100) cc_final: 0.8005 (m100) REVERT: C 695 GLN cc_start: 0.8516 (mt0) cc_final: 0.8211 (mt0) REVERT: C 722 LYS cc_start: 0.7199 (tptp) cc_final: 0.6978 (tptp) REVERT: C 740 THR cc_start: 0.6760 (m) cc_final: 0.6403 (m) REVERT: D 173 MET cc_start: 0.8815 (mtm) cc_final: 0.8286 (mtt) REVERT: D 198 ASP cc_start: 0.8102 (m-30) cc_final: 0.7168 (t70) REVERT: D 216 GLN cc_start: 0.8561 (tp-100) cc_final: 0.7935 (tp40) REVERT: D 251 ASN cc_start: 0.7930 (t0) cc_final: 0.7678 (t0) REVERT: D 257 GLU cc_start: 0.7758 (pt0) cc_final: 0.7468 (pt0) REVERT: D 285 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8616 (pp20) REVERT: D 332 GLU cc_start: 0.7077 (pt0) cc_final: 0.6766 (pp20) REVERT: D 335 THR cc_start: 0.9058 (p) cc_final: 0.8451 (t) REVERT: D 346 GLN cc_start: 0.9064 (mt0) cc_final: 0.8775 (mt0) REVERT: D 446 CYS cc_start: 0.8789 (m) cc_final: 0.8465 (t) REVERT: D 592 PHE cc_start: 0.8276 (t80) cc_final: 0.8031 (t80) REVERT: D 639 LEU cc_start: 0.8094 (tp) cc_final: 0.7350 (tp) REVERT: D 672 MET cc_start: 0.7823 (ttp) cc_final: 0.7269 (ttm) REVERT: D 695 GLN cc_start: 0.8515 (mt0) cc_final: 0.8213 (mt0) REVERT: D 740 THR cc_start: 0.6751 (m) cc_final: 0.6390 (m) outliers start: 4 outliers final: 0 residues processed: 712 average time/residue: 0.1360 time to fit residues: 153.1533 Evaluate side-chains 505 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 229 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 240 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 671 ASN C 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106696 restraints weight = 45282.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109539 restraints weight = 28281.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111507 restraints weight = 20192.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112885 restraints weight = 15854.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113682 restraints weight = 13357.646| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21460 Z= 0.164 Angle : 0.735 8.710 29032 Z= 0.387 Chirality : 0.043 0.258 3308 Planarity : 0.005 0.065 3624 Dihedral : 6.838 48.892 2808 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.98 % Favored : 85.86 % Rotamer: Outliers : 0.26 % Allowed : 2.70 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.15), residues: 2568 helix: -1.70 (0.12), residues: 1412 sheet: -4.46 (0.37), residues: 72 loop : -3.50 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.017 0.002 TYR B 382 PHE 0.018 0.001 PHE A 261 TRP 0.016 0.002 TRP D 692 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00355 (21460) covalent geometry : angle 0.73492 (29032) hydrogen bonds : bond 0.04836 ( 790) hydrogen bonds : angle 4.67688 ( 2292) *********************** 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 654 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 648 time to evaluate : 0.528 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: A 171 CYS cc_start: 0.8838 (p) cc_final: 0.8502 (p) REVERT: A 173 MET cc_start: 0.8736 (mtm) cc_final: 0.8212 (mtt) REVERT: A 198 ASP cc_start: 0.8076 (m-30) cc_final: 0.7140 (t70) REVERT: A 259 PHE cc_start: 0.8640 (t80) cc_final: 0.8412 (t80) REVERT: A 293 ASP cc_start: 0.8131 (t0) cc_final: 0.7781 (t0) REVERT: A 335 THR cc_start: 0.8968 (p) cc_final: 0.8328 (t) REVERT: A 346 GLN cc_start: 0.8965 (mt0) cc_final: 0.8658 (mt0) REVERT: A 446 CYS cc_start: 0.8668 (m) cc_final: 0.8468 (t) REVERT: A 488 MET cc_start: 0.8060 (ptp) cc_final: 0.7751 (ptp) REVERT: A 574 MET cc_start: 0.8689 (mmt) cc_final: 0.8081 (mmm) REVERT: A 639 LEU cc_start: 0.8076 (tp) cc_final: 0.7590 (tp) REVERT: A 672 MET cc_start: 0.7179 (tmm) cc_final: 0.6752 (tmm) REVERT: A 710 TRP cc_start: 0.7506 (m100) cc_final: 0.7302 (m100) REVERT: A 722 LYS cc_start: 0.7438 (tptp) cc_final: 0.7209 (tptp) REVERT: A 740 THR cc_start: 0.6547 (m) cc_final: 0.6249 (m) REVERT: B 171 CYS cc_start: 0.8859 (p) cc_final: 0.8533 (p) REVERT: B 173 MET cc_start: 0.8715 (mtm) cc_final: 0.8179 (mtt) REVERT: B 198 ASP cc_start: 0.8085 (m-30) cc_final: 0.7138 (t70) REVERT: B 230 ILE cc_start: 0.9616 (mt) cc_final: 0.9414 (mp) REVERT: B 259 PHE cc_start: 0.8672 (t80) cc_final: 0.8387 (t80) REVERT: B 293 ASP cc_start: 0.8105 (t0) cc_final: 0.7767 (t0) REVERT: B 332 GLU cc_start: 0.6858 (pt0) cc_final: 0.6613 (pp20) REVERT: B 335 THR cc_start: 0.8936 (p) cc_final: 0.8341 (t) REVERT: B 346 GLN cc_start: 0.8979 (mt0) cc_final: 0.8661 (mt0) REVERT: B 488 MET cc_start: 0.8102 (ptp) cc_final: 0.7841 (ptp) REVERT: B 574 MET cc_start: 0.8706 (mmt) cc_final: 0.8081 (mmm) REVERT: B 630 LEU cc_start: 0.9152 (mt) cc_final: 0.8951 (mm) REVERT: B 710 TRP cc_start: 0.7513 (m100) cc_final: 0.7283 (m100) REVERT: B 722 LYS cc_start: 0.7392 (tptp) cc_final: 0.7136 (tptp) REVERT: B 740 THR cc_start: 0.6564 (m) cc_final: 0.5825 (m) REVERT: C 171 CYS cc_start: 0.8880 (p) cc_final: 0.8540 (p) REVERT: C 173 MET cc_start: 0.8696 (mtm) cc_final: 0.8171 (mtt) REVERT: C 198 ASP cc_start: 0.8013 (m-30) cc_final: 0.7114 (t70) REVERT: C 230 ILE cc_start: 0.9620 (mt) cc_final: 0.9417 (mp) REVERT: C 293 ASP cc_start: 0.8114 (t0) cc_final: 0.7734 (t0) REVERT: C 332 GLU cc_start: 0.6866 (pt0) cc_final: 0.6624 (pp20) REVERT: C 335 THR cc_start: 0.8976 (p) cc_final: 0.8306 (t) REVERT: C 346 GLN cc_start: 0.8966 (mt0) cc_final: 0.8670 (mt0) REVERT: C 371 ARG cc_start: 0.8452 (ptt90) cc_final: 0.8111 (ttp80) REVERT: C 393 THR cc_start: 0.8748 (p) cc_final: 0.8510 (p) REVERT: C 574 MET cc_start: 0.8696 (mmt) cc_final: 0.8081 (mmm) REVERT: C 639 LEU cc_start: 0.8130 (tp) cc_final: 0.7754 (tp) REVERT: C 672 MET cc_start: 0.7788 (ttp) cc_final: 0.7518 (tmm) REVERT: C 676 LEU cc_start: 0.9232 (mp) cc_final: 0.8902 (mp) REVERT: C 710 TRP cc_start: 0.7560 (m100) cc_final: 0.7339 (m100) REVERT: C 722 LYS cc_start: 0.7387 (tptp) cc_final: 0.6998 (tptp) REVERT: C 740 THR cc_start: 0.6608 (m) cc_final: 0.5860 (m) REVERT: D 171 CYS cc_start: 0.8865 (p) cc_final: 0.8531 (p) REVERT: D 173 MET cc_start: 0.8646 (mtm) cc_final: 0.8157 (mtt) REVERT: D 198 ASP cc_start: 0.8075 (m-30) cc_final: 0.7146 (t70) REVERT: D 221 ILE cc_start: 0.9677 (tp) cc_final: 0.9462 (mm) REVERT: D 261 PHE cc_start: 0.7053 (m-10) cc_final: 0.6487 (m-80) REVERT: D 268 LEU cc_start: 0.9584 (tp) cc_final: 0.9298 (tp) REVERT: D 293 ASP cc_start: 0.8110 (t0) cc_final: 0.7745 (t0) REVERT: D 332 GLU cc_start: 0.6850 (pt0) cc_final: 0.6623 (pp20) REVERT: D 335 THR cc_start: 0.8962 (p) cc_final: 0.8310 (t) REVERT: D 346 GLN cc_start: 0.8977 (mt0) cc_final: 0.8687 (mt0) REVERT: D 574 MET cc_start: 0.8623 (mmt) cc_final: 0.8010 (mmm) REVERT: D 581 LYS cc_start: 0.9229 (tppp) cc_final: 0.9015 (ttpt) REVERT: D 672 MET cc_start: 0.7989 (ttp) cc_final: 0.7436 (ttm) REVERT: D 692 TRP cc_start: 0.9367 (t60) cc_final: 0.9162 (t60) REVERT: D 740 THR cc_start: 0.6486 (m) cc_final: 0.5776 (m) outliers start: 6 outliers final: 0 residues processed: 652 average time/residue: 0.1135 time to fit residues: 120.5866 Evaluate side-chains 490 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 76 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 671 ASN C 735 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 643 ASN D 647 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103666 restraints weight = 45800.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106347 restraints weight = 29312.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108221 restraints weight = 21324.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109536 restraints weight = 17044.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110453 restraints weight = 14551.135| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21460 Z= 0.205 Angle : 0.763 9.051 29032 Z= 0.399 Chirality : 0.045 0.222 3308 Planarity : 0.005 0.060 3624 Dihedral : 6.627 48.767 2808 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.80 % Favored : 85.05 % Rotamer: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.15), residues: 2568 helix: -1.09 (0.13), residues: 1400 sheet: -4.39 (0.36), residues: 76 loop : -3.52 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 226 TYR 0.019 0.002 TYR D 382 PHE 0.015 0.001 PHE C 666 TRP 0.016 0.002 TRP A 742 HIS 0.004 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00459 (21460) covalent geometry : angle 0.76324 (29032) hydrogen bonds : bond 0.04422 ( 790) hydrogen bonds : angle 4.59681 ( 2292) *********************** 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 621 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 616 time to evaluate : 0.646 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: A 159 MET cc_start: 0.8149 (mmt) cc_final: 0.7718 (mtt) REVERT: A 171 CYS cc_start: 0.8802 (p) cc_final: 0.8544 (p) REVERT: A 173 MET cc_start: 0.8615 (mtm) cc_final: 0.8161 (mtt) REVERT: A 198 ASP cc_start: 0.8029 (m-30) cc_final: 0.7106 (t70) REVERT: A 259 PHE cc_start: 0.8830 (t80) cc_final: 0.8580 (t80) REVERT: A 268 LEU cc_start: 0.9558 (tp) cc_final: 0.9014 (tp) REVERT: A 332 GLU cc_start: 0.7642 (pp20) cc_final: 0.7345 (pt0) REVERT: A 335 THR cc_start: 0.9033 (p) cc_final: 0.8384 (t) REVERT: A 346 GLN cc_start: 0.9026 (mt0) cc_final: 0.8697 (mt0) REVERT: A 371 ARG cc_start: 0.8458 (ptt90) cc_final: 0.8152 (ttp80) REVERT: A 488 MET cc_start: 0.8113 (ptp) cc_final: 0.7829 (ptp) REVERT: A 631 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 639 LEU cc_start: 0.8293 (tp) cc_final: 0.7539 (tp) REVERT: A 641 ASP cc_start: 0.5665 (p0) cc_final: 0.5267 (p0) REVERT: A 706 MET cc_start: 0.8563 (tpp) cc_final: 0.8102 (tpp) REVERT: B 159 MET cc_start: 0.8203 (mmt) cc_final: 0.7755 (mtt) REVERT: B 171 CYS cc_start: 0.8804 (p) cc_final: 0.8551 (p) REVERT: B 173 MET cc_start: 0.8636 (mtm) cc_final: 0.8164 (mtt) REVERT: B 198 ASP cc_start: 0.8046 (m-30) cc_final: 0.7099 (t70) REVERT: B 259 PHE cc_start: 0.8839 (t80) cc_final: 0.8597 (t80) REVERT: B 268 LEU cc_start: 0.9554 (tp) cc_final: 0.9012 (tp) REVERT: B 335 THR cc_start: 0.8927 (p) cc_final: 0.8320 (t) REVERT: B 346 GLN cc_start: 0.9015 (mt0) cc_final: 0.8704 (mt0) REVERT: B 488 MET cc_start: 0.8128 (ptp) cc_final: 0.7836 (ptp) REVERT: B 630 LEU cc_start: 0.9137 (mt) cc_final: 0.8927 (mm) REVERT: B 706 MET cc_start: 0.8536 (tpp) cc_final: 0.8073 (tpp) REVERT: C 159 MET cc_start: 0.8204 (mmt) cc_final: 0.7789 (mtt) REVERT: C 171 CYS cc_start: 0.8847 (p) cc_final: 0.8536 (p) REVERT: C 173 MET cc_start: 0.8605 (mtm) cc_final: 0.8158 (mtt) REVERT: C 198 ASP cc_start: 0.8057 (m-30) cc_final: 0.7103 (t70) REVERT: C 234 LEU cc_start: 0.9526 (mt) cc_final: 0.9315 (mt) REVERT: C 268 LEU cc_start: 0.9519 (tp) cc_final: 0.9127 (tp) REVERT: C 335 THR cc_start: 0.8954 (p) cc_final: 0.8326 (t) REVERT: C 346 GLN cc_start: 0.8996 (mt0) cc_final: 0.8693 (mt0) REVERT: C 371 ARG cc_start: 0.8464 (ptt90) cc_final: 0.8155 (ttp80) REVERT: C 488 MET cc_start: 0.8072 (ptp) cc_final: 0.7649 (ptp) REVERT: C 598 LEU cc_start: 0.8896 (tp) cc_final: 0.8607 (tp) REVERT: C 631 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7617 (mm-30) REVERT: C 639 LEU cc_start: 0.8272 (tp) cc_final: 0.7493 (tp) REVERT: C 641 ASP cc_start: 0.5679 (p0) cc_final: 0.5248 (p0) REVERT: C 672 MET cc_start: 0.8108 (ttp) cc_final: 0.7900 (tmm) REVERT: C 706 MET cc_start: 0.8537 (tpp) cc_final: 0.8048 (tpp) REVERT: D 159 MET cc_start: 0.8182 (mmt) cc_final: 0.7795 (mtt) REVERT: D 171 CYS cc_start: 0.8817 (p) cc_final: 0.8497 (p) REVERT: D 173 MET cc_start: 0.8603 (mtm) cc_final: 0.8216 (mtt) REVERT: D 198 ASP cc_start: 0.8154 (m-30) cc_final: 0.7147 (t70) REVERT: D 216 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8029 (tp40) REVERT: D 268 LEU cc_start: 0.9602 (tp) cc_final: 0.9254 (tp) REVERT: D 332 GLU cc_start: 0.6971 (pt0) cc_final: 0.6717 (pp20) REVERT: D 335 THR cc_start: 0.8966 (p) cc_final: 0.8325 (t) REVERT: D 346 GLN cc_start: 0.9045 (mt0) cc_final: 0.8709 (mt0) REVERT: D 488 MET cc_start: 0.8055 (ptp) cc_final: 0.7649 (ptp) outliers start: 5 outliers final: 0 residues processed: 620 average time/residue: 0.1115 time to fit residues: 113.7926 Evaluate side-chains 498 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 37 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 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 671 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104767 restraints weight = 45821.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107195 restraints weight = 30288.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108929 restraints weight = 22508.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110136 restraints weight = 18218.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110866 restraints weight = 15677.567| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21460 Z= 0.187 Angle : 0.733 7.989 29032 Z= 0.383 Chirality : 0.045 0.220 3308 Planarity : 0.005 0.057 3624 Dihedral : 6.497 48.798 2808 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.03 % Favored : 84.81 % Rotamer: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.16), residues: 2568 helix: -0.72 (0.13), residues: 1376 sheet: -4.37 (0.37), residues: 76 loop : -3.39 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 118 TYR 0.016 0.002 TYR D 382 PHE 0.027 0.001 PHE C 261 TRP 0.022 0.002 TRP D 493 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00423 (21460) covalent geometry : angle 0.73268 (29032) hydrogen bonds : bond 0.04205 ( 790) hydrogen bonds : angle 4.45988 ( 2292) *********************** 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 625 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 623 time to evaluate : 0.735 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: A 171 CYS cc_start: 0.8813 (p) cc_final: 0.8588 (p) REVERT: A 173 MET cc_start: 0.8590 (mtm) cc_final: 0.8113 (mtt) REVERT: A 198 ASP cc_start: 0.8064 (m-30) cc_final: 0.7118 (t70) REVERT: A 261 PHE cc_start: 0.7216 (m-80) cc_final: 0.6707 (m-80) REVERT: A 268 LEU cc_start: 0.9610 (tp) cc_final: 0.9306 (tp) REVERT: A 293 ASP cc_start: 0.8512 (t0) cc_final: 0.8007 (t0) REVERT: A 332 GLU cc_start: 0.7613 (pp20) cc_final: 0.7373 (pt0) REVERT: A 335 THR cc_start: 0.8944 (p) cc_final: 0.8294 (t) REVERT: A 346 GLN cc_start: 0.8954 (mt0) cc_final: 0.8666 (mt0) REVERT: A 371 ARG cc_start: 0.8437 (ptt90) cc_final: 0.8151 (ttp80) REVERT: A 488 MET cc_start: 0.8155 (ptp) cc_final: 0.7727 (ptp) REVERT: A 639 LEU cc_start: 0.8276 (tp) cc_final: 0.7774 (tp) REVERT: A 672 MET cc_start: 0.7202 (tmm) cc_final: 0.6868 (tmm) REVERT: A 706 MET cc_start: 0.8599 (tpp) cc_final: 0.8175 (tpp) REVERT: A 719 GLU cc_start: 0.8309 (pt0) cc_final: 0.8090 (pm20) REVERT: B 171 CYS cc_start: 0.8811 (p) cc_final: 0.8594 (p) REVERT: B 173 MET cc_start: 0.8569 (mtm) cc_final: 0.8073 (mtt) REVERT: B 198 ASP cc_start: 0.8078 (m-30) cc_final: 0.7115 (t70) REVERT: B 261 PHE cc_start: 0.7237 (m-80) cc_final: 0.6663 (m-80) REVERT: B 268 LEU cc_start: 0.9614 (tp) cc_final: 0.9308 (tp) REVERT: B 293 ASP cc_start: 0.8481 (t0) cc_final: 0.7993 (t0) REVERT: B 335 THR cc_start: 0.8889 (p) cc_final: 0.8249 (t) REVERT: B 346 GLN cc_start: 0.8942 (mt0) cc_final: 0.8671 (mt0) REVERT: B 488 MET cc_start: 0.8183 (ptp) cc_final: 0.7736 (ptp) REVERT: B 630 LEU cc_start: 0.9146 (mt) cc_final: 0.8933 (mm) REVERT: B 706 MET cc_start: 0.8517 (tpp) cc_final: 0.8109 (tpp) REVERT: C 171 CYS cc_start: 0.8829 (p) cc_final: 0.8586 (p) REVERT: C 173 MET cc_start: 0.8580 (mtm) cc_final: 0.8037 (mtt) REVERT: C 198 ASP cc_start: 0.8073 (m-30) cc_final: 0.7089 (t70) REVERT: C 216 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7714 (tp40) REVERT: C 251 ASN cc_start: 0.8088 (t0) cc_final: 0.7573 (t0) REVERT: C 268 LEU cc_start: 0.9617 (tp) cc_final: 0.9384 (tp) REVERT: C 293 ASP cc_start: 0.8421 (t0) cc_final: 0.8082 (t0) REVERT: C 322 ASP cc_start: 0.8513 (t70) cc_final: 0.8182 (t0) REVERT: C 335 THR cc_start: 0.8888 (p) cc_final: 0.8257 (t) REVERT: C 371 ARG cc_start: 0.8399 (ptt90) cc_final: 0.8151 (ttp80) REVERT: C 488 MET cc_start: 0.8160 (ptp) cc_final: 0.7574 (ptp) REVERT: C 598 LEU cc_start: 0.8853 (tp) cc_final: 0.8630 (tp) REVERT: C 639 LEU cc_start: 0.8304 (tp) cc_final: 0.7784 (tp) REVERT: C 672 MET cc_start: 0.8146 (ttp) cc_final: 0.7764 (tmm) REVERT: C 676 LEU cc_start: 0.9171 (mp) cc_final: 0.8964 (mp) REVERT: C 706 MET cc_start: 0.8580 (tpp) cc_final: 0.8159 (tpp) REVERT: D 171 CYS cc_start: 0.8804 (p) cc_final: 0.8547 (p) REVERT: D 173 MET cc_start: 0.8588 (mtm) cc_final: 0.8159 (mtt) REVERT: D 198 ASP cc_start: 0.8059 (m-30) cc_final: 0.7091 (t70) REVERT: D 268 LEU cc_start: 0.9615 (tp) cc_final: 0.9367 (tp) REVERT: D 335 THR cc_start: 0.8908 (p) cc_final: 0.8299 (t) REVERT: D 488 MET cc_start: 0.8142 (ptp) cc_final: 0.7560 (ptp) REVERT: D 706 MET cc_start: 0.8640 (tpp) cc_final: 0.8203 (tpp) outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.1115 time to fit residues: 114.7029 Evaluate side-chains 506 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 157 optimal weight: 0.7980 chunk 170 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 647 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108136 restraints weight = 45297.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110931 restraints weight = 28712.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112886 restraints weight = 20797.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114279 restraints weight = 16505.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115155 restraints weight = 13998.795| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21460 Z= 0.140 Angle : 0.693 8.417 29032 Z= 0.360 Chirality : 0.043 0.215 3308 Planarity : 0.004 0.056 3624 Dihedral : 6.233 48.538 2808 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.71 % Favored : 86.14 % Rotamer: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.16), residues: 2568 helix: -0.43 (0.14), residues: 1364 sheet: -3.84 (0.43), residues: 68 loop : -3.27 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.013 0.001 TYR A 359 PHE 0.023 0.001 PHE D 527 TRP 0.017 0.001 TRP C 493 HIS 0.005 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00302 (21460) covalent geometry : angle 0.69294 (29032) hydrogen bonds : bond 0.03700 ( 790) hydrogen bonds : angle 4.18711 ( 2292) *********************** 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 634 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 632 time to evaluate : 0.717 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 173 MET cc_start: 0.8565 (mtm) cc_final: 0.8181 (mtt) REVERT: A 198 ASP cc_start: 0.8094 (m-30) cc_final: 0.7084 (t70) REVERT: A 268 LEU cc_start: 0.9634 (tp) cc_final: 0.9299 (tp) REVERT: A 335 THR cc_start: 0.8946 (p) cc_final: 0.8334 (t) REVERT: A 346 GLN cc_start: 0.8900 (mt0) cc_final: 0.8640 (mt0) REVERT: A 371 ARG cc_start: 0.8541 (ptt90) cc_final: 0.8246 (ttp80) REVERT: A 488 MET cc_start: 0.8143 (ptp) cc_final: 0.7738 (ptp) REVERT: A 562 MET cc_start: 0.8947 (mmt) cc_final: 0.8485 (mmt) REVERT: A 639 LEU cc_start: 0.8170 (tp) cc_final: 0.7677 (tp) REVERT: A 705 LYS cc_start: 0.9114 (mttp) cc_final: 0.8575 (tmtt) REVERT: A 706 MET cc_start: 0.8661 (tpp) cc_final: 0.8165 (tpp) REVERT: A 717 MET cc_start: 0.5792 (tpp) cc_final: 0.5591 (tpp) REVERT: B 173 MET cc_start: 0.8566 (mtm) cc_final: 0.8179 (mtt) REVERT: B 198 ASP cc_start: 0.8112 (m-30) cc_final: 0.7098 (t70) REVERT: B 268 LEU cc_start: 0.9637 (tp) cc_final: 0.9308 (tp) REVERT: B 322 ASP cc_start: 0.8388 (t70) cc_final: 0.8087 (t0) REVERT: B 335 THR cc_start: 0.8991 (p) cc_final: 0.8369 (t) REVERT: B 346 GLN cc_start: 0.8898 (mt0) cc_final: 0.8636 (mt0) REVERT: B 488 MET cc_start: 0.8173 (ptp) cc_final: 0.7711 (ptp) REVERT: B 562 MET cc_start: 0.8934 (mmt) cc_final: 0.8462 (mmt) REVERT: B 630 LEU cc_start: 0.9157 (mt) cc_final: 0.8926 (mm) REVERT: B 702 GLU cc_start: 0.8469 (tp30) cc_final: 0.8248 (tp30) REVERT: B 705 LYS cc_start: 0.9082 (mttp) cc_final: 0.8519 (tmtt) REVERT: B 706 MET cc_start: 0.8602 (tpp) cc_final: 0.8099 (tpp) REVERT: C 173 MET cc_start: 0.8590 (mtm) cc_final: 0.8137 (mtt) REVERT: C 198 ASP cc_start: 0.8075 (m-30) cc_final: 0.7083 (t70) REVERT: C 268 LEU cc_start: 0.9606 (tp) cc_final: 0.9311 (tp) REVERT: C 322 ASP cc_start: 0.8423 (t70) cc_final: 0.8155 (t0) REVERT: C 335 THR cc_start: 0.8909 (p) cc_final: 0.8281 (t) REVERT: C 488 MET cc_start: 0.8149 (ptp) cc_final: 0.7720 (ptp) REVERT: C 562 MET cc_start: 0.8953 (mmt) cc_final: 0.8464 (mmt) REVERT: C 598 LEU cc_start: 0.8834 (tp) cc_final: 0.8564 (tp) REVERT: C 639 LEU cc_start: 0.8175 (tp) cc_final: 0.7681 (tp) REVERT: C 672 MET cc_start: 0.8117 (ttp) cc_final: 0.7741 (tmm) REVERT: C 702 GLU cc_start: 0.8500 (tp30) cc_final: 0.8292 (tp30) REVERT: C 705 LYS cc_start: 0.9076 (mttp) cc_final: 0.8558 (tmtt) REVERT: C 706 MET cc_start: 0.8692 (tpp) cc_final: 0.7868 (tpp) REVERT: C 717 MET cc_start: 0.7303 (tpt) cc_final: 0.6906 (tpp) REVERT: D 173 MET cc_start: 0.8573 (mtm) cc_final: 0.8164 (mtt) REVERT: D 198 ASP cc_start: 0.8093 (m-30) cc_final: 0.7122 (t70) REVERT: D 259 PHE cc_start: 0.8494 (t80) cc_final: 0.8060 (t80) REVERT: D 268 LEU cc_start: 0.9609 (tp) cc_final: 0.9264 (tp) REVERT: D 335 THR cc_start: 0.8883 (p) cc_final: 0.8282 (t) REVERT: D 393 THR cc_start: 0.8765 (p) cc_final: 0.8316 (p) REVERT: D 488 MET cc_start: 0.8127 (ptp) cc_final: 0.7714 (ptp) REVERT: D 562 MET cc_start: 0.8985 (mmt) cc_final: 0.8504 (mmt) REVERT: D 702 GLU cc_start: 0.8483 (tp30) cc_final: 0.8234 (tp30) REVERT: D 705 LYS cc_start: 0.9106 (mttp) cc_final: 0.8531 (tmtt) REVERT: D 706 MET cc_start: 0.8684 (tpp) cc_final: 0.7854 (tpp) outliers start: 2 outliers final: 0 residues processed: 632 average time/residue: 0.1153 time to fit residues: 119.0827 Evaluate side-chains 519 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 139 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 671 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105756 restraints weight = 45447.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108478 restraints weight = 28973.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110369 restraints weight = 21011.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111715 restraints weight = 16720.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112517 restraints weight = 14180.569| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21460 Z= 0.171 Angle : 0.721 8.025 29032 Z= 0.373 Chirality : 0.045 0.248 3308 Planarity : 0.005 0.056 3624 Dihedral : 6.213 47.854 2808 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.02 % Favored : 85.71 % Rotamer: Outliers : 0.09 % Allowed : 1.52 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.16), residues: 2568 helix: -0.33 (0.14), residues: 1368 sheet: -4.21 (0.44), residues: 68 loop : -3.33 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 716 TYR 0.017 0.002 TYR B 382 PHE 0.031 0.002 PHE C 261 TRP 0.020 0.002 TRP D 710 HIS 0.005 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00391 (21460) covalent geometry : angle 0.72115 (29032) hydrogen bonds : bond 0.03820 ( 790) hydrogen bonds : angle 4.28841 ( 2292) *********************** 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 615 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 613 time to evaluate : 0.761 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: A 173 MET cc_start: 0.8614 (mtm) cc_final: 0.8168 (mtt) REVERT: A 198 ASP cc_start: 0.8124 (m-30) cc_final: 0.7170 (t70) REVERT: A 202 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8303 (mtm110) REVERT: A 322 ASP cc_start: 0.8620 (t0) cc_final: 0.8281 (t0) REVERT: A 335 THR cc_start: 0.8984 (p) cc_final: 0.8303 (t) REVERT: A 346 GLN cc_start: 0.8985 (mt0) cc_final: 0.8671 (mt0) REVERT: A 359 TYR cc_start: 0.8917 (t80) cc_final: 0.8335 (t80) REVERT: A 488 MET cc_start: 0.8231 (ptp) cc_final: 0.7816 (ptp) REVERT: A 562 MET cc_start: 0.8978 (mmt) cc_final: 0.8483 (mmt) REVERT: A 639 LEU cc_start: 0.8334 (tp) cc_final: 0.7827 (tp) REVERT: A 705 LYS cc_start: 0.9131 (mttp) cc_final: 0.8581 (tmtt) REVERT: A 706 MET cc_start: 0.8689 (tpp) cc_final: 0.8266 (tpp) REVERT: B 159 MET cc_start: 0.8288 (mmt) cc_final: 0.8071 (mmm) REVERT: B 173 MET cc_start: 0.8598 (mtm) cc_final: 0.8155 (mtt) REVERT: B 198 ASP cc_start: 0.8133 (m-30) cc_final: 0.7112 (t70) REVERT: B 335 THR cc_start: 0.8923 (p) cc_final: 0.8319 (t) REVERT: B 346 GLN cc_start: 0.9015 (mt0) cc_final: 0.8651 (mt0) REVERT: B 371 ARG cc_start: 0.8629 (ptt90) cc_final: 0.8116 (ttp80) REVERT: B 488 MET cc_start: 0.8198 (ptp) cc_final: 0.7753 (ptp) REVERT: B 702 GLU cc_start: 0.8537 (tp30) cc_final: 0.8300 (tp30) REVERT: B 705 LYS cc_start: 0.9126 (mttp) cc_final: 0.8573 (tmtt) REVERT: B 706 MET cc_start: 0.8680 (tpp) cc_final: 0.8251 (tpp) REVERT: C 173 MET cc_start: 0.8629 (mtm) cc_final: 0.8141 (mtt) REVERT: C 198 ASP cc_start: 0.8400 (m-30) cc_final: 0.7144 (t0) REVERT: C 335 THR cc_start: 0.8945 (p) cc_final: 0.8334 (t) REVERT: C 488 MET cc_start: 0.8218 (ptp) cc_final: 0.7797 (ptp) REVERT: C 598 LEU cc_start: 0.8876 (tp) cc_final: 0.8659 (tp) REVERT: C 672 MET cc_start: 0.8264 (ttp) cc_final: 0.7835 (tmm) REVERT: C 676 LEU cc_start: 0.9196 (mp) cc_final: 0.8956 (mp) REVERT: C 702 GLU cc_start: 0.8558 (tp30) cc_final: 0.8308 (tp30) REVERT: C 705 LYS cc_start: 0.9123 (mttp) cc_final: 0.8609 (tmtt) REVERT: C 706 MET cc_start: 0.8686 (tpp) cc_final: 0.7962 (tpp) REVERT: D 134 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 138 LEU cc_start: 0.8908 (mt) cc_final: 0.8475 (mt) REVERT: D 173 MET cc_start: 0.8617 (mtm) cc_final: 0.8202 (mtt) REVERT: D 198 ASP cc_start: 0.8416 (m-30) cc_final: 0.7178 (t0) REVERT: D 335 THR cc_start: 0.8910 (p) cc_final: 0.8322 (t) REVERT: D 393 THR cc_start: 0.8859 (p) cc_final: 0.8494 (m) REVERT: D 488 MET cc_start: 0.8203 (ptp) cc_final: 0.7756 (ptp) REVERT: D 702 GLU cc_start: 0.8543 (tp30) cc_final: 0.8306 (tp30) REVERT: D 705 LYS cc_start: 0.9126 (mttp) cc_final: 0.8559 (tmtt) REVERT: D 706 MET cc_start: 0.8658 (tpp) cc_final: 0.7956 (tpp) REVERT: D 717 MET cc_start: 0.5987 (ttt) cc_final: 0.5739 (tpp) outliers start: 2 outliers final: 0 residues processed: 613 average time/residue: 0.1186 time to fit residues: 118.4029 Evaluate side-chains 497 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 242 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN A 671 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108428 restraints weight = 44849.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111164 restraints weight = 28645.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113147 restraints weight = 20836.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114417 restraints weight = 16542.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115451 restraints weight = 14102.085| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21460 Z= 0.137 Angle : 0.696 8.051 29032 Z= 0.358 Chirality : 0.043 0.243 3308 Planarity : 0.004 0.056 3624 Dihedral : 6.089 48.247 2808 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.90 % Favored : 85.90 % Rotamer: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.16), residues: 2568 helix: -0.11 (0.14), residues: 1420 sheet: -3.60 (0.64), residues: 44 loop : -3.47 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.017 0.001 TYR C 359 PHE 0.029 0.001 PHE D 259 TRP 0.020 0.002 TRP A 493 HIS 0.005 0.001 HIS B 745 Details of bonding type rmsd covalent geometry : bond 0.00307 (21460) covalent geometry : angle 0.69648 (29032) hydrogen bonds : bond 0.03505 ( 790) hydrogen bonds : angle 4.17356 ( 2292) *********************** 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 629 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 627 time to evaluate : 0.584 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: 0.8590 (mtm) cc_final: 0.8173 (mtt) REVERT: A 198 ASP cc_start: 0.8111 (m-30) cc_final: 0.7121 (t0) REVERT: A 251 ASN cc_start: 0.8232 (t0) cc_final: 0.7709 (t0) REVERT: A 268 LEU cc_start: 0.9599 (tp) cc_final: 0.9063 (tp) REVERT: A 322 ASP cc_start: 0.8498 (t0) cc_final: 0.8233 (t0) REVERT: A 335 THR cc_start: 0.8932 (p) cc_final: 0.8317 (t) REVERT: A 359 TYR cc_start: 0.8806 (t80) cc_final: 0.8285 (t80) REVERT: A 485 LEU cc_start: 0.8505 (tt) cc_final: 0.8244 (tp) REVERT: A 488 MET cc_start: 0.8202 (ptp) cc_final: 0.7795 (ptp) REVERT: A 562 MET cc_start: 0.8928 (mmt) cc_final: 0.8469 (mmt) REVERT: A 639 LEU cc_start: 0.8245 (tp) cc_final: 0.7736 (tp) REVERT: A 705 LYS cc_start: 0.9114 (mttp) cc_final: 0.8573 (tmtt) REVERT: A 706 MET cc_start: 0.8634 (tpp) cc_final: 0.8191 (tpp) REVERT: B 134 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 138 LEU cc_start: 0.8911 (mt) cc_final: 0.8500 (mt) REVERT: B 173 MET cc_start: 0.8588 (mtm) cc_final: 0.8165 (mtt) REVERT: B 198 ASP cc_start: 0.8100 (m-30) cc_final: 0.7043 (t0) REVERT: B 251 ASN cc_start: 0.8240 (t0) cc_final: 0.7711 (t0) REVERT: B 268 LEU cc_start: 0.9585 (tp) cc_final: 0.9070 (tp) REVERT: B 335 THR cc_start: 0.8954 (p) cc_final: 0.8382 (t) REVERT: B 346 GLN cc_start: 0.8854 (mt0) cc_final: 0.8629 (mt0) REVERT: B 371 ARG cc_start: 0.8572 (ptt90) cc_final: 0.8086 (ttp80) REVERT: B 488 MET cc_start: 0.8183 (ptp) cc_final: 0.7737 (ptp) REVERT: B 705 LYS cc_start: 0.9121 (mttp) cc_final: 0.8568 (tmtt) REVERT: B 706 MET cc_start: 0.8644 (tpp) cc_final: 0.7933 (tpp) REVERT: C 155 PRO cc_start: 0.8648 (Cg_endo) cc_final: 0.8390 (Cg_exo) REVERT: C 173 MET cc_start: 0.8585 (mtm) cc_final: 0.8209 (mtt) REVERT: C 198 ASP cc_start: 0.8371 (m-30) cc_final: 0.7035 (t0) REVERT: C 251 ASN cc_start: 0.8245 (t0) cc_final: 0.7714 (t0) REVERT: C 268 LEU cc_start: 0.9562 (tp) cc_final: 0.9121 (tp) REVERT: C 335 THR cc_start: 0.8878 (p) cc_final: 0.8316 (t) REVERT: C 488 MET cc_start: 0.8176 (ptp) cc_final: 0.7772 (ptp) REVERT: C 598 LEU cc_start: 0.8834 (tp) cc_final: 0.8615 (tp) REVERT: C 639 LEU cc_start: 0.8246 (tp) cc_final: 0.7772 (tp) REVERT: C 702 GLU cc_start: 0.8507 (tp30) cc_final: 0.8248 (tp30) REVERT: C 705 LYS cc_start: 0.9116 (mttp) cc_final: 0.8589 (tmtt) REVERT: C 706 MET cc_start: 0.8635 (tpp) cc_final: 0.7900 (tpp) REVERT: D 134 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 138 LEU cc_start: 0.8889 (mt) cc_final: 0.8482 (mt) REVERT: D 155 PRO cc_start: 0.8729 (Cg_endo) cc_final: 0.8497 (Cg_exo) REVERT: D 173 MET cc_start: 0.8597 (mtm) cc_final: 0.8230 (mtt) REVERT: D 198 ASP cc_start: 0.8397 (m-30) cc_final: 0.7045 (t0) REVERT: D 251 ASN cc_start: 0.8126 (t0) cc_final: 0.7562 (t0) REVERT: D 335 THR cc_start: 0.8872 (p) cc_final: 0.8302 (t) REVERT: D 393 THR cc_start: 0.8829 (p) cc_final: 0.8591 (m) REVERT: D 488 MET cc_start: 0.8134 (ptp) cc_final: 0.7790 (ptp) REVERT: D 639 LEU cc_start: 0.8147 (tp) cc_final: 0.7921 (tp) REVERT: D 705 LYS cc_start: 0.9096 (mttp) cc_final: 0.8537 (tmtt) REVERT: D 706 MET cc_start: 0.8620 (tpp) cc_final: 0.7928 (tpp) outliers start: 2 outliers final: 0 residues processed: 627 average time/residue: 0.1172 time to fit residues: 119.3883 Evaluate side-chains 516 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 5.9990 chunk 253 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109627 restraints weight = 44054.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112338 restraints weight = 27844.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114281 restraints weight = 20012.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115614 restraints weight = 15733.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116429 restraints weight = 13232.558| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21460 Z= 0.144 Angle : 0.712 11.156 29032 Z= 0.364 Chirality : 0.044 0.247 3308 Planarity : 0.004 0.053 3624 Dihedral : 6.052 47.853 2808 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.86 % Favored : 85.90 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.16), residues: 2568 helix: -0.03 (0.14), residues: 1416 sheet: -3.94 (0.50), residues: 68 loop : -3.43 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.018 0.001 TYR D 359 PHE 0.034 0.001 PHE D 261 TRP 0.023 0.002 TRP A 742 HIS 0.005 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00329 (21460) covalent geometry : angle 0.71185 (29032) hydrogen bonds : bond 0.03488 ( 790) hydrogen bonds : angle 4.22497 ( 2292) *********************** 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 633 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 632 time to evaluate : 0.713 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 134 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 138 LEU cc_start: 0.8940 (mt) cc_final: 0.8518 (mt) REVERT: A 173 MET cc_start: 0.8609 (mtm) cc_final: 0.8175 (mtt) REVERT: A 198 ASP cc_start: 0.8256 (m-30) cc_final: 0.7059 (t0) REVERT: A 251 ASN cc_start: 0.8115 (t0) cc_final: 0.7615 (t0) REVERT: A 322 ASP cc_start: 0.8532 (t0) cc_final: 0.8318 (t0) REVERT: A 335 THR cc_start: 0.8944 (p) cc_final: 0.8322 (t) REVERT: A 346 GLN cc_start: 0.8873 (mt0) cc_final: 0.8667 (mt0) REVERT: A 359 TYR cc_start: 0.8786 (t80) cc_final: 0.8286 (t80) REVERT: A 488 MET cc_start: 0.8212 (ptp) cc_final: 0.7774 (ptp) REVERT: A 639 LEU cc_start: 0.8232 (tp) cc_final: 0.7749 (tp) REVERT: A 705 LYS cc_start: 0.9136 (mttp) cc_final: 0.8596 (tmtt) REVERT: A 706 MET cc_start: 0.8645 (tpp) cc_final: 0.8193 (tpp) REVERT: A 719 GLU cc_start: 0.7579 (pm20) cc_final: 0.7196 (pt0) REVERT: A 722 LYS cc_start: 0.6352 (tptm) cc_final: 0.5530 (tptm) REVERT: B 134 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 138 LEU cc_start: 0.8915 (mt) cc_final: 0.8503 (mt) REVERT: B 173 MET cc_start: 0.8581 (mtm) cc_final: 0.8138 (mtt) REVERT: B 198 ASP cc_start: 0.8064 (m-30) cc_final: 0.6996 (t70) REVERT: B 251 ASN cc_start: 0.8140 (t0) cc_final: 0.7621 (t0) REVERT: B 322 ASP cc_start: 0.8526 (t0) cc_final: 0.8290 (t0) REVERT: B 335 THR cc_start: 0.8945 (p) cc_final: 0.8372 (t) REVERT: B 346 GLN cc_start: 0.8851 (mt0) cc_final: 0.8633 (mt0) REVERT: B 359 TYR cc_start: 0.8862 (t80) cc_final: 0.8294 (t80) REVERT: B 371 ARG cc_start: 0.8623 (ptt90) cc_final: 0.8114 (ttp80) REVERT: B 488 MET cc_start: 0.8142 (ptp) cc_final: 0.7771 (ptp) REVERT: B 705 LYS cc_start: 0.9103 (mttp) cc_final: 0.8558 (tmtt) REVERT: B 706 MET cc_start: 0.8665 (tpp) cc_final: 0.8211 (tpp) REVERT: C 134 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7800 (tm-30) REVERT: C 138 LEU cc_start: 0.8928 (mt) cc_final: 0.8507 (mt) REVERT: C 173 MET cc_start: 0.8622 (mtm) cc_final: 0.8188 (mtt) REVERT: C 198 ASP cc_start: 0.8372 (m-30) cc_final: 0.7001 (t70) REVERT: C 248 VAL cc_start: 0.9321 (m) cc_final: 0.8992 (p) REVERT: C 251 ASN cc_start: 0.8199 (t0) cc_final: 0.7727 (t0) REVERT: C 322 ASP cc_start: 0.8523 (t0) cc_final: 0.8274 (t0) REVERT: C 335 THR cc_start: 0.8961 (p) cc_final: 0.8387 (t) REVERT: C 359 TYR cc_start: 0.8866 (t80) cc_final: 0.8334 (t80) REVERT: C 485 LEU cc_start: 0.8516 (tt) cc_final: 0.8262 (tp) REVERT: C 488 MET cc_start: 0.8168 (ptp) cc_final: 0.7778 (ptp) REVERT: C 598 LEU cc_start: 0.8877 (tp) cc_final: 0.8637 (tp) REVERT: C 705 LYS cc_start: 0.9125 (mttp) cc_final: 0.8602 (tmtt) REVERT: C 706 MET cc_start: 0.8659 (tpp) cc_final: 0.7921 (tpp) REVERT: D 134 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 138 LEU cc_start: 0.8905 (mt) cc_final: 0.8473 (mt) REVERT: D 155 PRO cc_start: 0.8779 (Cg_endo) cc_final: 0.8568 (Cg_exo) REVERT: D 173 MET cc_start: 0.8611 (mtm) cc_final: 0.8190 (mtt) REVERT: D 198 ASP cc_start: 0.8372 (m-30) cc_final: 0.7016 (t70) REVERT: D 251 ASN cc_start: 0.8136 (t0) cc_final: 0.7644 (t0) REVERT: D 322 ASP cc_start: 0.8544 (t70) cc_final: 0.7894 (t0) REVERT: D 335 THR cc_start: 0.8923 (p) cc_final: 0.8405 (t) REVERT: D 359 TYR cc_start: 0.8942 (t80) cc_final: 0.8624 (t80) REVERT: D 485 LEU cc_start: 0.8497 (tt) cc_final: 0.8229 (tp) REVERT: D 488 MET cc_start: 0.8151 (ptp) cc_final: 0.7716 (ptp) REVERT: D 639 LEU cc_start: 0.8151 (tp) cc_final: 0.7911 (tp) REVERT: D 705 LYS cc_start: 0.9071 (mttp) cc_final: 0.8541 (tmtt) REVERT: D 706 MET cc_start: 0.8725 (tpp) cc_final: 0.7996 (tpp) REVERT: D 717 MET cc_start: 0.5910 (ttt) cc_final: 0.5576 (tpp) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.1146 time to fit residues: 118.8596 Evaluate side-chains 532 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 86 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 0.3980 chunk 249 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 683 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN C 683 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107077 restraints weight = 45145.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109803 restraints weight = 28892.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111704 restraints weight = 21029.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113062 restraints weight = 16775.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113986 restraints weight = 14255.710| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21460 Z= 0.161 Angle : 0.724 8.514 29032 Z= 0.371 Chirality : 0.045 0.250 3308 Planarity : 0.005 0.054 3624 Dihedral : 6.003 47.408 2808 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.63 % Favored : 86.06 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.16), residues: 2568 helix: -0.01 (0.13), residues: 1428 sheet: -3.91 (0.52), residues: 68 loop : -3.36 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 375 TYR 0.022 0.001 TYR D 382 PHE 0.027 0.001 PHE D 259 TRP 0.025 0.002 TRP D 742 HIS 0.005 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00371 (21460) covalent geometry : angle 0.72372 (29032) hydrogen bonds : bond 0.03562 ( 790) hydrogen bonds : angle 4.28058 ( 2292) ********************** 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 613 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 611 time to evaluate : 0.815 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: A 134 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 138 LEU cc_start: 0.8930 (mt) cc_final: 0.8504 (mt) REVERT: A 173 MET cc_start: 0.8549 (mtm) cc_final: 0.8107 (mtt) REVERT: A 198 ASP cc_start: 0.8259 (m-30) cc_final: 0.7064 (t0) REVERT: A 251 ASN cc_start: 0.8293 (t0) cc_final: 0.7777 (t0) REVERT: A 268 LEU cc_start: 0.9603 (tp) cc_final: 0.8986 (tp) REVERT: A 322 ASP cc_start: 0.8523 (t0) cc_final: 0.8292 (t0) REVERT: A 335 THR cc_start: 0.8927 (p) cc_final: 0.8321 (t) REVERT: A 359 TYR cc_start: 0.8833 (t80) cc_final: 0.8281 (t80) REVERT: A 488 MET cc_start: 0.8210 (ptp) cc_final: 0.7786 (ptp) REVERT: A 630 LEU cc_start: 0.9227 (mt) cc_final: 0.8999 (mm) REVERT: A 639 LEU cc_start: 0.8283 (tp) cc_final: 0.7785 (tp) REVERT: A 705 LYS cc_start: 0.9090 (mttp) cc_final: 0.8595 (tmtt) REVERT: A 706 MET cc_start: 0.8677 (tpp) cc_final: 0.8216 (tpp) REVERT: A 722 LYS cc_start: 0.6404 (tptm) cc_final: 0.5447 (tptm) REVERT: B 134 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 138 LEU cc_start: 0.8913 (mt) cc_final: 0.8484 (mt) REVERT: B 173 MET cc_start: 0.8626 (mtm) cc_final: 0.8248 (mtt) REVERT: B 198 ASP cc_start: 0.8072 (m-30) cc_final: 0.7011 (t70) REVERT: B 216 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7724 (tp40) REVERT: B 251 ASN cc_start: 0.8311 (t0) cc_final: 0.7793 (t0) REVERT: B 268 LEU cc_start: 0.9587 (tp) cc_final: 0.9102 (tp) REVERT: B 322 ASP cc_start: 0.8525 (t0) cc_final: 0.8241 (t0) REVERT: B 335 THR cc_start: 0.8961 (p) cc_final: 0.8386 (t) REVERT: B 346 GLN cc_start: 0.8907 (mt0) cc_final: 0.8618 (mt0) REVERT: B 359 TYR cc_start: 0.8879 (t80) cc_final: 0.8304 (t80) REVERT: B 371 ARG cc_start: 0.8633 (ptt90) cc_final: 0.8131 (ttp80) REVERT: B 488 MET cc_start: 0.8211 (ptp) cc_final: 0.7762 (ptp) REVERT: B 705 LYS cc_start: 0.9117 (mttp) cc_final: 0.8584 (tmtt) REVERT: B 706 MET cc_start: 0.8685 (tpp) cc_final: 0.8234 (tpp) REVERT: C 152 LEU cc_start: 0.7010 (tt) cc_final: 0.6600 (mm) REVERT: C 173 MET cc_start: 0.8625 (mtm) cc_final: 0.8198 (mtt) REVERT: C 198 ASP cc_start: 0.8195 (m-30) cc_final: 0.6889 (t70) REVERT: C 248 VAL cc_start: 0.9221 (m) cc_final: 0.8892 (p) REVERT: C 251 ASN cc_start: 0.8344 (t0) cc_final: 0.7866 (t0) REVERT: C 322 ASP cc_start: 0.8601 (t0) cc_final: 0.8262 (t0) REVERT: C 335 THR cc_start: 0.8958 (p) cc_final: 0.8388 (t) REVERT: C 359 TYR cc_start: 0.8889 (t80) cc_final: 0.8318 (t80) REVERT: C 488 MET cc_start: 0.8205 (ptp) cc_final: 0.7759 (ptp) REVERT: C 630 LEU cc_start: 0.9224 (mt) cc_final: 0.9005 (mm) REVERT: C 639 LEU cc_start: 0.8283 (tp) cc_final: 0.7824 (tp) REVERT: C 705 LYS cc_start: 0.9077 (mttp) cc_final: 0.8567 (tmtt) REVERT: C 706 MET cc_start: 0.8644 (tpp) cc_final: 0.8228 (tpp) REVERT: D 152 LEU cc_start: 0.7047 (tt) cc_final: 0.6558 (mm) REVERT: D 155 PRO cc_start: 0.8784 (Cg_endo) cc_final: 0.8570 (Cg_exo) REVERT: D 173 MET cc_start: 0.8622 (mtm) cc_final: 0.8131 (mmm) REVERT: D 198 ASP cc_start: 0.8342 (m-30) cc_final: 0.6999 (t70) REVERT: D 248 VAL cc_start: 0.9186 (m) cc_final: 0.8873 (p) REVERT: D 251 ASN cc_start: 0.8240 (t0) cc_final: 0.7744 (t0) REVERT: D 322 ASP cc_start: 0.8521 (t70) cc_final: 0.8009 (t0) REVERT: D 335 THR cc_start: 0.8891 (p) cc_final: 0.8319 (t) REVERT: D 359 TYR cc_start: 0.8957 (t80) cc_final: 0.8239 (t80) REVERT: D 485 LEU cc_start: 0.8519 (tt) cc_final: 0.8282 (tp) REVERT: D 488 MET cc_start: 0.8166 (ptp) cc_final: 0.7677 (ptp) REVERT: D 639 LEU cc_start: 0.8167 (tp) cc_final: 0.7928 (tp) REVERT: D 705 LYS cc_start: 0.9102 (mttp) cc_final: 0.8544 (tmtt) REVERT: D 706 MET cc_start: 0.8718 (tpp) cc_final: 0.8298 (tpp) outliers start: 2 outliers final: 0 residues processed: 611 average time/residue: 0.1159 time to fit residues: 115.2044 Evaluate side-chains 532 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 213 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107290 restraints weight = 45197.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110028 restraints weight = 28977.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111953 restraints weight = 21070.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113320 restraints weight = 16781.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114007 restraints weight = 14240.319| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21460 Z= 0.152 Angle : 0.720 9.143 29032 Z= 0.368 Chirality : 0.045 0.246 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.981 47.174 2808 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.86 % Favored : 85.83 % Rotamer: Outliers : 0.09 % Allowed : 0.48 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.16), residues: 2568 helix: 0.05 (0.14), residues: 1420 sheet: -3.87 (0.52), residues: 68 loop : -3.34 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 TYR 0.018 0.001 TYR D 359 PHE 0.035 0.001 PHE A 259 TRP 0.022 0.002 TRP A 742 HIS 0.005 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00349 (21460) covalent geometry : angle 0.71972 (29032) hydrogen bonds : bond 0.03514 ( 790) hydrogen bonds : angle 4.30770 ( 2292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.99 seconds wall clock time: 54 minutes 35.83 seconds (3275.83 seconds total)