Starting phenix.real_space_refine (version: dev) on Thu Feb 23 20:16:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvw_8919/02_2023/6dvw_8919.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21004 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Time building chain proxies: 12.45, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 8.62 Conformation dependent library (CDL) restraints added in 3.1 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 62.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 117 through 130 removed outlier: 4.437A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.008A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.900A pdb=" N PHE A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 251 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.701A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.611A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.798A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.516A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 501 removed outlier: 4.077A pdb=" N LEU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.504A pdb=" N GLN A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.745A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.724A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.437A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.695A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.210A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.899A pdb=" N PHE B 250 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 251 " --> pdb=" O VAL B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 251' Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.610A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.650A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.607A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.516A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.505A pdb=" N GLN B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.744A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.725A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 612' Processing helix chain 'B' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 removed outlier: 4.438A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 5.129A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 removed outlier: 3.800A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.900A pdb=" N PHE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 251' Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.609A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.517A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.995A pdb=" N LEU C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 508 removed outlier: 4.330A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.504A pdb=" N GLN C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.744A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.725A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.051A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.080A pdb=" N LYS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 623 through 638 removed outlier: 4.174A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 658 through 676 removed outlier: 3.549A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 4.438A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.696A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 5.128A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.009A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.954A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.134A pdb=" N GLU D 214 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.799A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.211A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.899A pdb=" N PHE D 250 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D 251 " --> pdb=" O VAL D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 251' Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.690A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.700A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.610A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.799A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.651A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.606A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.517A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 457 removed outlier: 3.994A pdb=" N LEU D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 501 removed outlier: 4.078A pdb=" N LEU D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.329A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 515 removed outlier: 3.505A pdb=" N GLN D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 543 removed outlier: 3.507A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.745A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.724A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.716A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.052A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 612 removed outlier: 4.081A pdb=" N LYS D 611 " --> pdb=" O SER D 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 607 through 612' Processing helix chain 'D' and resid 623 through 638 removed outlier: 4.173A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 656 Processing helix chain 'D' and resid 658 through 676 removed outlier: 3.550A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET D 672 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 4.362A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 790 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 9.32 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: 98.15 - 105.32: 343 105.32 - 112.50: 10577 112.50 - 119.67: 8054 119.67 - 126.84: 9746 126.84 - 134.01: 312 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 2.800 nonbonded pdb=" SG CYS D 612 " pdb=" OG1 THR D 649 " model vdw 1.841 2.800 nonbonded pdb=" SG CYS B 612 " pdb=" OG1 THR B 649 " model vdw 1.841 2.800 nonbonded pdb=" SG CYS A 612 " pdb=" OG1 THR A 649 " model vdw 1.841 2.800 nonbonded pdb=" O LEU A 608 " pdb=" OG SER A 613 " model vdw 2.212 2.440 ... (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 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 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. 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: 0.710 Set stop_for_unknowns flag: 0.010 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: 4.580 Check model and map are aligned: 0.350 Process input model: 53.680 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 21460 Z= 0.537 Angle : 1.191 11.113 29032 Z= 0.645 Chirality : 0.061 0.314 3308 Planarity : 0.008 0.081 3624 Dihedral : 11.878 74.777 7920 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.89 % Favored : 83.72 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.12), residues: 2568 helix: -3.94 (0.08), residues: 1256 sheet: -4.64 (0.29), residues: 68 loop : -3.68 (0.15), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 765 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 773 average time/residue: 0.2947 time to fit residues: 355.1489 Evaluate side-chains 471 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 463 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1722 time to fit residues: 5.9464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 483 GLN A 643 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 297 ASN B 483 GLN B 643 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 483 GLN C 643 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 297 ASN D 483 GLN D 643 ASN D 671 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 21460 Z= 0.228 Angle : 0.794 9.290 29032 Z= 0.414 Chirality : 0.044 0.243 3308 Planarity : 0.006 0.088 3624 Dihedral : 7.276 49.122 2808 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.98 % Favored : 85.86 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.14), residues: 2568 helix: -2.36 (0.11), residues: 1388 sheet: -4.61 (0.32), residues: 76 loop : -3.43 (0.18), residues: 1104 *********************** 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 689 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 681 time to evaluate : 2.435 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 outliers start: 8 outliers final: 0 residues processed: 685 average time/residue: 0.2959 time to fit residues: 317.9130 Evaluate side-chains 490 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 0.0020 chunk 251 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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 D 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21460 Z= 0.199 Angle : 0.732 8.981 29032 Z= 0.380 Chirality : 0.042 0.215 3308 Planarity : 0.005 0.066 3624 Dihedral : 6.760 48.792 2808 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.17 % Favored : 85.67 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.15), residues: 2568 helix: -1.69 (0.12), residues: 1416 sheet: -4.38 (0.35), residues: 72 loop : -3.48 (0.17), residues: 1080 *********************** 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 637 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 634 time to evaluate : 2.582 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 outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.2844 time to fit residues: 290.5470 Evaluate side-chains 467 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 483 GLN B 671 ASN C 273 ASN C 671 ASN C 735 ASN D 273 ASN D 643 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 21460 Z= 0.191 Angle : 0.701 9.196 29032 Z= 0.365 Chirality : 0.042 0.221 3308 Planarity : 0.005 0.062 3624 Dihedral : 6.477 48.187 2808 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.43 % Favored : 86.41 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.15), residues: 2568 helix: -1.14 (0.13), residues: 1396 sheet: -4.12 (0.39), residues: 72 loop : -3.40 (0.17), residues: 1100 *********************** 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 614 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 611 time to evaluate : 2.537 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 outliers start: 3 outliers final: 0 residues processed: 611 average time/residue: 0.2802 time to fit residues: 281.8110 Evaluate side-chains 481 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 171 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 483 GLN C 178 ASN C 273 ASN C 483 GLN C 671 ASN D 178 ASN D 273 ASN D 483 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21460 Z= 0.187 Angle : 0.686 8.442 29032 Z= 0.354 Chirality : 0.042 0.219 3308 Planarity : 0.004 0.060 3624 Dihedral : 6.235 47.680 2808 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.14 % Favored : 85.71 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.16), residues: 2568 helix: -0.65 (0.14), residues: 1368 sheet: -4.02 (0.40), residues: 76 loop : -3.22 (0.17), residues: 1124 *********************** 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 616 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 2.757 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 outliers start: 1 outliers final: 0 residues processed: 615 average time/residue: 0.2791 time to fit residues: 279.6082 Evaluate side-chains 490 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN B 178 ASN B 585 HIS C 671 ASN D 643 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21460 Z= 0.186 Angle : 0.686 8.337 29032 Z= 0.353 Chirality : 0.042 0.224 3308 Planarity : 0.004 0.058 3624 Dihedral : 6.129 47.275 2808 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.43 % Favored : 86.41 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2568 helix: -0.43 (0.14), residues: 1384 sheet: -3.84 (0.43), residues: 76 loop : -3.27 (0.17), residues: 1108 *********************** 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 614 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 612 time to evaluate : 2.517 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 outliers start: 2 outliers final: 0 residues processed: 612 average time/residue: 0.2803 time to fit residues: 278.8187 Evaluate side-chains 482 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN B 647 ASN C 647 ASN C 671 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21460 Z= 0.224 Angle : 0.698 8.360 29032 Z= 0.358 Chirality : 0.043 0.212 3308 Planarity : 0.005 0.056 3624 Dihedral : 6.083 46.550 2808 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.33 % Favored : 85.51 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 2568 helix: -0.36 (0.14), residues: 1404 sheet: -3.82 (0.44), residues: 76 loop : -3.30 (0.18), residues: 1088 *********************** 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 588 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 586 time to evaluate : 2.706 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 outliers start: 2 outliers final: 0 residues processed: 586 average time/residue: 0.2851 time to fit residues: 272.5623 Evaluate side-chains 460 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 0.0470 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 647 ASN A 671 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 585 HIS C 647 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 21460 Z= 0.179 Angle : 0.693 8.298 29032 Z= 0.352 Chirality : 0.042 0.205 3308 Planarity : 0.004 0.055 3624 Dihedral : 5.983 46.341 2808 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2568 helix: -0.31 (0.14), residues: 1452 sheet: -3.57 (0.50), residues: 68 loop : -3.23 (0.18), residues: 1048 *********************** 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 594 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 0.2838 time to fit residues: 271.2266 Evaluate side-chains 482 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 0.3980 chunk 215 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 180 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS A 647 ASN A 671 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 21460 Z= 0.173 Angle : 0.700 8.330 29032 Z= 0.353 Chirality : 0.042 0.197 3308 Planarity : 0.004 0.053 3624 Dihedral : 5.943 46.635 2808 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.17 % Favored : 85.67 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2568 helix: -0.09 (0.14), residues: 1436 sheet: -3.38 (0.54), residues: 68 loop : -2.98 (0.19), residues: 1064 *********************** 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 615 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 614 time to evaluate : 2.449 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 outliers start: 1 outliers final: 0 residues processed: 614 average time/residue: 0.2755 time to fit residues: 276.3203 Evaluate side-chains 493 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 161 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 647 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 21460 Z= 0.180 Angle : 0.700 8.428 29032 Z= 0.353 Chirality : 0.043 0.248 3308 Planarity : 0.004 0.062 3624 Dihedral : 5.835 46.272 2808 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.06 % Favored : 85.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2568 helix: -0.04 (0.14), residues: 1436 sheet: -3.26 (0.56), residues: 68 loop : -2.90 (0.19), residues: 1064 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 2.759 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 outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.2749 time to fit residues: 266.5718 Evaluate side-chains 492 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.799 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 647 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 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 = 0.3608 r_free = 0.3608 target = 0.133139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109218 restraints weight = 45721.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111984 restraints weight = 29315.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113927 restraints weight = 21349.499| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 21460 Z= 0.233 Angle : 0.729 9.078 29032 Z= 0.370 Chirality : 0.044 0.242 3308 Planarity : 0.005 0.061 3624 Dihedral : 5.854 45.498 2808 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.52 % Favored : 85.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2568 helix: 0.03 (0.14), residues: 1404 sheet: -3.24 (0.56), residues: 68 loop : -2.93 (0.18), residues: 1096 =============================================================================== Job complete usr+sys time: 4976.79 seconds wall clock time: 90 minutes 11.99 seconds (5411.99 seconds total)