Starting phenix.real_space_refine on Thu Feb 22 17:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl6_24518/02_2024/7rl6_24518_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21858 2.51 5 N 6144 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34854 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.35, per 1000 atoms: 0.50 Number of scatterers: 34854 At special positions: 0 Unit cell: (178.2, 173.138, 99.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6648 8.00 N 6144 7.00 C 21858 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.06 Conformation dependent library (CDL) restraints added in 6.6 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 48 sheets defined 37.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.123A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.718A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.779A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.501A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.631A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 387 removed outlier: 4.018A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.847A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.617A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.827A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.520A pdb=" N ARG A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.086A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.636A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.009A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.897A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 removed outlier: 3.805A pdb=" N LEU A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.859A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 684 through 704 removed outlier: 3.647A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 737 No H-bonds generated for 'chain 'A' and resid 734 through 737' Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.122A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.718A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.779A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.502A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.631A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 387 removed outlier: 4.018A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.847A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.618A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.827A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 444' Processing helix chain 'B' and resid 449 through 458 removed outlier: 3.521A pdb=" N ARG B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 526 through 534 removed outlier: 4.086A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 547 No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.637A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 558 through 568 removed outlier: 4.009A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.897A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 609 removed outlier: 3.805A pdb=" N LEU B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.859A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 Processing helix chain 'B' and resid 684 through 704 removed outlier: 3.646A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 737 No H-bonds generated for 'chain 'B' and resid 734 through 737' Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.122A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.719A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.778A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.501A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.631A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 387 removed outlier: 4.018A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 removed outlier: 3.847A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.617A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.827A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 444' Processing helix chain 'C' and resid 449 through 458 removed outlier: 3.520A pdb=" N ARG C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 526 through 534 removed outlier: 4.087A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.636A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 558 through 568 removed outlier: 4.008A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 removed outlier: 3.897A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 3.805A pdb=" N LEU C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.860A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 677 Processing helix chain 'C' and resid 684 through 704 removed outlier: 3.647A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 737 No H-bonds generated for 'chain 'C' and resid 734 through 737' Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.122A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.717A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.779A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.502A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.632A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 387 removed outlier: 4.018A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 removed outlier: 3.848A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.618A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.826A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 444' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.520A pdb=" N ARG D 453 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 526 through 534 removed outlier: 4.087A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 547 No H-bonds generated for 'chain 'D' and resid 544 through 547' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.637A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 558 through 568 removed outlier: 4.009A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 3.897A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 removed outlier: 3.803A pdb=" N LEU D 605 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.860A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 677 Processing helix chain 'D' and resid 684 through 704 removed outlier: 3.647A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 737 No H-bonds generated for 'chain 'D' and resid 734 through 737' Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 4.122A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.718A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.778A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU E 221 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.501A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.632A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 387 removed outlier: 4.018A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 removed outlier: 3.847A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.617A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.828A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 444' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.521A pdb=" N ARG E 453 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 493 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 526 through 534 removed outlier: 4.087A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 547 No H-bonds generated for 'chain 'E' and resid 544 through 547' Processing helix chain 'E' and resid 549 through 553 removed outlier: 3.636A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 549 through 553' Processing helix chain 'E' and resid 558 through 568 removed outlier: 4.008A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE E 563 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 3.897A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 609 removed outlier: 3.804A pdb=" N LEU E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR E 606 " --> pdb=" O ASN E 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET E 608 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.859A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 677 Processing helix chain 'E' and resid 684 through 704 removed outlier: 3.647A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 737 No H-bonds generated for 'chain 'E' and resid 734 through 737' Processing helix chain 'E' and resid 740 through 742 No H-bonds generated for 'chain 'E' and resid 740 through 742' Processing helix chain 'E' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.122A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 removed outlier: 3.718A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.779A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.502A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.631A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 387 removed outlier: 4.017A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 removed outlier: 3.846A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 430 removed outlier: 3.617A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.827A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 439 through 444' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.520A pdb=" N ARG F 453 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.657A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 526 through 534 removed outlier: 4.087A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 547 No H-bonds generated for 'chain 'F' and resid 544 through 547' Processing helix chain 'F' and resid 549 through 553 removed outlier: 3.636A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 549 through 553' Processing helix chain 'F' and resid 558 through 568 removed outlier: 4.009A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE F 563 " --> pdb=" O VAL F 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 3.896A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 609 removed outlier: 3.805A pdb=" N LEU F 605 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR F 606 " --> pdb=" O ASN F 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET F 608 " --> pdb=" O ILE F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 662 removed outlier: 3.860A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 677 Processing helix chain 'F' and resid 684 through 704 removed outlier: 3.647A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 737 No H-bonds generated for 'chain 'F' and resid 734 through 737' Processing helix chain 'F' and resid 740 through 742 No H-bonds generated for 'chain 'F' and resid 740 through 742' Processing helix chain 'F' and resid 749 through 763 removed outlier: 3.890A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.645A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.214A pdb=" N ILE A 82 " --> pdb=" O ASP A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= D, first strand: chain 'A' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL A 181 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL A 116 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS A 183 " --> pdb=" O VAL A 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.716A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL A 468 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.273A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.645A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.215A pdb=" N ILE B 82 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= L, first strand: chain 'B' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL B 116 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS B 183 " --> pdb=" O VAL B 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.716A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL B 468 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.273A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.645A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.215A pdb=" N ILE C 82 " --> pdb=" O ASP C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= T, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL C 181 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 116 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS C 183 " --> pdb=" O VAL C 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.715A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL C 468 " --> pdb=" O SER C 541 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.272A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.644A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.214A pdb=" N ILE D 82 " --> pdb=" O ASP D 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 39 through 41 Processing sheet with id= AB, first strand: chain 'D' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL D 181 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL D 116 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS D 183 " --> pdb=" O VAL D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.715A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL D 468 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.272A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 25 through 27 removed outlier: 3.644A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 28 through 30 removed outlier: 6.214A pdb=" N ILE E 82 " --> pdb=" O ASP E 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= AJ, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL E 181 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 116 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS E 183 " --> pdb=" O VAL E 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.716A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL E 468 " --> pdb=" O SER E 541 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.272A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.644A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 28 through 30 removed outlier: 6.214A pdb=" N ILE F 82 " --> pdb=" O ASP F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AR, first strand: chain 'F' and resid 113 through 116 removed outlier: 6.864A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 116 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS F 183 " --> pdb=" O VAL F 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'F' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.715A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL F 468 " --> pdb=" O SER F 541 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.273A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2232 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: 11.70 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11897 1.34 - 1.46: 5904 1.46 - 1.58: 17335 1.58 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35460 Sorted by residual: bond pdb=" C4 ADP D1001 " pdb=" C5 ADP D1001 " ideal model delta sigma weight residual 1.490 1.453 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" C4 ADP F1001 " pdb=" C5 ADP F1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.455 0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 35455 not shown) Histogram of bond angle deviations from ideal: 98.46 - 106.10: 1061 106.10 - 113.75: 19770 113.75 - 121.39: 17541 121.39 - 129.03: 9424 129.03 - 136.67: 156 Bond angle restraints: 47952 Sorted by residual: angle pdb=" C SER B 171 " pdb=" N PRO B 172 " pdb=" CD PRO B 172 " ideal model delta sigma weight residual 120.60 112.76 7.84 2.20e+00 2.07e-01 1.27e+01 angle pdb=" C SER F 171 " pdb=" N PRO F 172 " pdb=" CD PRO F 172 " ideal model delta sigma weight residual 120.60 112.79 7.81 2.20e+00 2.07e-01 1.26e+01 angle pdb=" C SER E 171 " pdb=" N PRO E 172 " pdb=" CD PRO E 172 " ideal model delta sigma weight residual 120.60 112.82 7.78 2.20e+00 2.07e-01 1.25e+01 angle pdb=" C SER C 171 " pdb=" N PRO C 172 " pdb=" CD PRO C 172 " ideal model delta sigma weight residual 120.60 112.82 7.78 2.20e+00 2.07e-01 1.25e+01 angle pdb=" C SER D 171 " pdb=" N PRO D 172 " pdb=" CD PRO D 172 " ideal model delta sigma weight residual 120.60 112.83 7.77 2.20e+00 2.07e-01 1.25e+01 ... (remaining 47947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 21148 32.54 - 65.09: 687 65.09 - 97.63: 55 97.63 - 130.17: 10 130.17 - 162.72: 6 Dihedral angle restraints: 21906 sinusoidal: 9222 harmonic: 12684 Sorted by residual: dihedral pdb=" O1B ADP C1002 " pdb=" O3A ADP C1002 " pdb=" PB ADP C1002 " pdb=" PA ADP C1002 " ideal model delta sinusoidal sigma weight residual 300.00 137.28 162.72 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP E1002 " pdb=" O3A ADP E1002 " pdb=" PB ADP E1002 " pdb=" PA ADP E1002 " ideal model delta sinusoidal sigma weight residual 300.00 141.55 158.45 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP D1002 " pdb=" O3A ADP D1002 " pdb=" PA ADP D1002 " pdb=" PB ADP D1002 " ideal model delta sinusoidal sigma weight residual -60.00 96.86 -156.86 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 21903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2724 0.027 - 0.054: 1698 0.054 - 0.082: 460 0.082 - 0.109: 356 0.109 - 0.136: 138 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CA MET F 332 " pdb=" N MET F 332 " pdb=" C MET F 332 " pdb=" CB MET F 332 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA MET D 332 " pdb=" N MET D 332 " pdb=" C MET D 332 " pdb=" CB MET D 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA MET A 332 " pdb=" N MET A 332 " pdb=" C MET A 332 " pdb=" CB MET A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 271 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 271 " -0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 271 " -0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO E 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 272 " -0.050 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 296 2.53 - 3.12: 25516 3.12 - 3.72: 54724 3.72 - 4.31: 72272 4.31 - 4.90: 117309 Nonbonded interactions: 270117 Sorted by model distance: nonbonded pdb=" N LYS A 524 " pdb=" O2B ADP A1002 " model vdw 1.941 2.496 nonbonded pdb=" N LYS E 524 " pdb=" O2B ADP E1002 " model vdw 1.967 2.496 nonbonded pdb=" N LYS B 524 " pdb=" O2B ADP B1002 " model vdw 1.969 2.496 nonbonded pdb=" CB LYS C 524 " pdb=" O2B ADP C1002 " model vdw 2.010 2.752 nonbonded pdb=" CG LYS C 524 " pdb=" O2B ADP C1002 " model vdw 2.064 3.440 ... (remaining 270112 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.530 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 86.190 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.003 0.037 35460 Z= 0.181 Angle : 0.724 7.844 47952 Z= 0.385 Chirality : 0.044 0.136 5376 Planarity : 0.004 0.091 6300 Dihedral : 15.387 162.719 13686 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.88 % Favored : 94.85 % Rotamer: Outliers : 0.32 % Allowed : 0.64 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4386 helix: -1.44 (0.13), residues: 1416 sheet: 0.01 (0.23), residues: 546 loop : -1.32 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 454 HIS 0.004 0.001 HIS B 340 PHE 0.017 0.001 PHE E 452 TYR 0.021 0.001 TYR A 173 ARG 0.004 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 3.982 Fit side-chains REVERT: A 46 MET cc_start: 0.7150 (tpp) cc_final: 0.6947 (tpp) REVERT: B 46 MET cc_start: 0.7245 (tpp) cc_final: 0.7023 (tpp) REVERT: B 275 MET cc_start: 0.8423 (mpp) cc_final: 0.8105 (mpp) REVERT: B 601 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6899 (mm) REVERT: C 46 MET cc_start: 0.6990 (tpp) cc_final: 0.6772 (tpp) REVERT: C 275 MET cc_start: 0.8365 (mpp) cc_final: 0.8120 (mpp) REVERT: D 46 MET cc_start: 0.6908 (tpp) cc_final: 0.6693 (tpp) REVERT: D 198 LEU cc_start: 0.9335 (tt) cc_final: 0.8821 (tt) REVERT: E 46 MET cc_start: 0.7308 (tpp) cc_final: 0.7088 (tpp) REVERT: E 601 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6763 (mm) REVERT: E 757 MET cc_start: 0.9084 (ptt) cc_final: 0.8827 (ppp) REVERT: F 46 MET cc_start: 0.7089 (tpp) cc_final: 0.6884 (tpp) REVERT: F 601 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6762 (mm) REVERT: F 678 MET cc_start: 0.8645 (ppp) cc_final: 0.8418 (ppp) outliers start: 12 outliers final: 2 residues processed: 200 average time/residue: 0.4285 time to fit residues: 147.4022 Evaluate side-chains 157 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 40.0000 chunk 331 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 397 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 215 GLN A 351 ASN B 36 ASN B 215 GLN B 351 ASN C 36 ASN C 351 ASN D 36 ASN D 215 GLN D 351 ASN E 36 ASN E 351 ASN F 36 ASN F 351 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35460 Z= 0.280 Angle : 0.678 12.666 47952 Z= 0.316 Chirality : 0.046 0.155 5376 Planarity : 0.004 0.090 6300 Dihedral : 8.448 134.588 4924 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.83 % Favored : 95.90 % Rotamer: Outliers : 0.51 % Allowed : 6.83 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4386 helix: -1.17 (0.13), residues: 1458 sheet: -0.53 (0.21), residues: 642 loop : -1.03 (0.14), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 551 HIS 0.004 0.001 HIS C 340 PHE 0.016 0.002 PHE A 360 TYR 0.016 0.002 TYR A 173 ARG 0.008 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 4.013 Fit side-chains REVERT: A 427 MET cc_start: 0.7613 (tpt) cc_final: 0.7363 (tpt) REVERT: B 275 MET cc_start: 0.8810 (mpp) cc_final: 0.8495 (mmm) REVERT: B 608 MET cc_start: 0.9356 (ptp) cc_final: 0.8901 (ptp) REVERT: C 275 MET cc_start: 0.8826 (mpp) cc_final: 0.8389 (mpp) REVERT: D 427 MET cc_start: 0.7422 (tpt) cc_final: 0.7205 (tpt) REVERT: E 427 MET cc_start: 0.7700 (tpt) cc_final: 0.7480 (tpt) REVERT: E 757 MET cc_start: 0.9154 (ptt) cc_final: 0.8890 (ppp) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.4136 time to fit residues: 114.8685 Evaluate side-chains 151 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 392 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 331 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 398 optimal weight: 0.0000 chunk 430 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 395 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN E 215 GLN E 602 ASN F 36 ASN F 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35460 Z= 0.189 Angle : 0.589 13.329 47952 Z= 0.268 Chirality : 0.044 0.143 5376 Planarity : 0.004 0.083 6300 Dihedral : 7.830 119.975 4914 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.21 % Rotamer: Outliers : 1.07 % Allowed : 9.23 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4386 helix: -0.65 (0.13), residues: 1548 sheet: -0.26 (0.21), residues: 636 loop : -1.12 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 551 HIS 0.002 0.000 HIS F 340 PHE 0.013 0.001 PHE C 516 TYR 0.014 0.001 TYR A 173 ARG 0.003 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 4.440 Fit side-chains REVERT: A 46 MET cc_start: 0.7495 (tpp) cc_final: 0.7239 (tpp) REVERT: A 382 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: A 678 MET cc_start: 0.8783 (ppp) cc_final: 0.8495 (ppp) REVERT: B 46 MET cc_start: 0.7685 (tpp) cc_final: 0.7428 (tpp) REVERT: B 608 MET cc_start: 0.9364 (ptp) cc_final: 0.8916 (ptp) REVERT: C 46 MET cc_start: 0.7375 (tpp) cc_final: 0.7110 (tpp) REVERT: C 382 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: D 46 MET cc_start: 0.7314 (tpp) cc_final: 0.7036 (tpp) REVERT: D 381 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9075 (mm) REVERT: D 382 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: D 427 MET cc_start: 0.7616 (tpt) cc_final: 0.7389 (tpt) REVERT: D 678 MET cc_start: 0.8883 (ppp) cc_final: 0.8660 (ppp) REVERT: E 46 MET cc_start: 0.7711 (tpp) cc_final: 0.7461 (tpp) REVERT: E 608 MET cc_start: 0.9393 (ptp) cc_final: 0.8871 (ptp) REVERT: E 757 MET cc_start: 0.9179 (ptt) cc_final: 0.8947 (ppp) REVERT: F 46 MET cc_start: 0.7599 (tpp) cc_final: 0.7369 (tpp) outliers start: 40 outliers final: 23 residues processed: 165 average time/residue: 0.4127 time to fit residues: 121.5145 Evaluate side-chains 156 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 3.9990 chunk 299 optimal weight: 0.1980 chunk 206 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 190 optimal weight: 0.3980 chunk 267 optimal weight: 9.9990 chunk 399 optimal weight: 0.8980 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 379 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN C 602 ASN E 270 ASN F 270 ASN F 602 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35460 Z= 0.148 Angle : 0.573 8.555 47952 Z= 0.257 Chirality : 0.043 0.205 5376 Planarity : 0.004 0.087 6300 Dihedral : 7.266 109.224 4914 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.88 % Favored : 95.85 % Rotamer: Outliers : 1.57 % Allowed : 11.17 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4386 helix: -0.39 (0.14), residues: 1518 sheet: -0.12 (0.21), residues: 636 loop : -1.07 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 551 HIS 0.002 0.000 HIS B 340 PHE 0.010 0.001 PHE F 516 TYR 0.012 0.001 TYR A 173 ARG 0.002 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 133 time to evaluate : 3.840 Fit side-chains REVERT: A 275 MET cc_start: 0.8580 (mpp) cc_final: 0.8130 (mpp) REVERT: A 382 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: B 605 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 608 MET cc_start: 0.9376 (ptp) cc_final: 0.8940 (ptp) REVERT: C 46 MET cc_start: 0.7316 (tpp) cc_final: 0.7113 (tpt) REVERT: C 382 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: D 381 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (mm) REVERT: D 382 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: D 427 MET cc_start: 0.7695 (tpt) cc_final: 0.7486 (tpt) REVERT: E 605 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8866 (pp) REVERT: E 608 MET cc_start: 0.9406 (ptp) cc_final: 0.8888 (ptp) REVERT: E 757 MET cc_start: 0.9197 (ptt) cc_final: 0.8959 (ppp) REVERT: F 84 MET cc_start: 0.7280 (ttt) cc_final: 0.6934 (tmm) outliers start: 59 outliers final: 34 residues processed: 171 average time/residue: 0.4089 time to fit residues: 124.1407 Evaluate side-chains 170 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.0770 chunk 240 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 315 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 292 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 216 optimal weight: 20.0000 chunk 380 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 3.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 ASN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35460 Z= 0.245 Angle : 0.625 12.507 47952 Z= 0.285 Chirality : 0.044 0.157 5376 Planarity : 0.004 0.083 6300 Dihedral : 6.892 105.945 4914 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.08 % Favored : 95.65 % Rotamer: Outliers : 2.45 % Allowed : 11.95 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4386 helix: -0.26 (0.13), residues: 1608 sheet: -0.10 (0.21), residues: 648 loop : -1.02 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 551 HIS 0.005 0.001 HIS F 384 PHE 0.015 0.002 PHE A 452 TYR 0.010 0.001 TYR A 173 ARG 0.006 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 135 time to evaluate : 4.400 Fit side-chains REVERT: A 46 MET cc_start: 0.8075 (tpt) cc_final: 0.7849 (tpp) REVERT: A 382 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8781 (pm20) REVERT: B 46 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: B 605 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8918 (pp) REVERT: B 608 MET cc_start: 0.9438 (ptp) cc_final: 0.8978 (ptp) REVERT: B 678 MET cc_start: 0.8923 (ppp) cc_final: 0.8690 (ppp) REVERT: C 382 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: D 46 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7165 (tpt) REVERT: D 382 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8760 (pm20) REVERT: D 608 MET cc_start: 0.9261 (ptp) cc_final: 0.8975 (ptp) REVERT: E 605 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8981 (pp) REVERT: E 608 MET cc_start: 0.9472 (ptp) cc_final: 0.9016 (ptp) REVERT: E 757 MET cc_start: 0.9224 (ptt) cc_final: 0.9017 (ppp) REVERT: F 84 MET cc_start: 0.7022 (ttt) cc_final: 0.6701 (tmm) REVERT: F 678 MET cc_start: 0.8826 (ppp) cc_final: 0.8374 (ppp) outliers start: 92 outliers final: 62 residues processed: 202 average time/residue: 0.3965 time to fit residues: 143.3380 Evaluate side-chains 195 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 126 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 7.9990 chunk 381 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 248 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 423 optimal weight: 5.9990 chunk 351 optimal weight: 0.2980 chunk 196 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 602 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 35460 Z= 0.395 Angle : 0.736 12.924 47952 Z= 0.348 Chirality : 0.047 0.192 5376 Planarity : 0.005 0.088 6300 Dihedral : 6.740 79.117 4914 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.83 % Favored : 95.78 % Rotamer: Outliers : 2.61 % Allowed : 13.57 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.91 (0.13), residues: 4386 helix: -0.26 (0.13), residues: 1614 sheet: 0.03 (0.21), residues: 624 loop : -0.99 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 551 HIS 0.005 0.001 HIS A 384 PHE 0.026 0.003 PHE C 516 TYR 0.014 0.002 TYR F 755 ARG 0.009 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 141 time to evaluate : 4.117 Fit side-chains revert: symmetry clash REVERT: A 163 PHE cc_start: 0.6882 (t80) cc_final: 0.6467 (t80) REVERT: A 382 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: B 442 MET cc_start: 0.9386 (mmm) cc_final: 0.9107 (mpp) REVERT: B 605 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9136 (pp) REVERT: B 608 MET cc_start: 0.9507 (ptp) cc_final: 0.9097 (ptp) REVERT: C 163 PHE cc_start: 0.7065 (t80) cc_final: 0.6418 (t80) REVERT: D 117 LEU cc_start: 0.8348 (tp) cc_final: 0.8041 (tt) REVERT: D 163 PHE cc_start: 0.7047 (t80) cc_final: 0.6304 (t80) REVERT: E 605 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9205 (pp) REVERT: E 608 MET cc_start: 0.9543 (ptp) cc_final: 0.9104 (ptp) REVERT: F 46 MET cc_start: 0.8220 (mtt) cc_final: 0.7205 (tpp) REVERT: F 678 MET cc_start: 0.8861 (ppp) cc_final: 0.8633 (ppp) outliers start: 98 outliers final: 68 residues processed: 213 average time/residue: 0.4027 time to fit residues: 152.7196 Evaluate side-chains 204 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 133 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 241 optimal weight: 0.6980 chunk 309 optimal weight: 8.9990 chunk 239 optimal weight: 0.0870 chunk 356 optimal weight: 20.0000 chunk 236 optimal weight: 0.2980 chunk 422 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35460 Z= 0.230 Angle : 0.635 14.176 47952 Z= 0.289 Chirality : 0.045 0.224 5376 Planarity : 0.004 0.080 6300 Dihedral : 6.448 68.837 4914 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.38 % Favored : 95.35 % Rotamer: Outliers : 2.45 % Allowed : 14.59 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.81 (0.13), residues: 4386 helix: -0.15 (0.13), residues: 1662 sheet: -0.17 (0.21), residues: 648 loop : -0.88 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 551 HIS 0.003 0.001 HIS A 406 PHE 0.017 0.001 PHE B 516 TYR 0.013 0.001 TYR E 755 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 140 time to evaluate : 4.433 Fit side-chains REVERT: A 46 MET cc_start: 0.7913 (tpt) cc_final: 0.7561 (tpp) REVERT: A 84 MET cc_start: 0.7298 (ttp) cc_final: 0.7076 (ttt) REVERT: A 163 PHE cc_start: 0.6870 (t80) cc_final: 0.6445 (t80) REVERT: A 275 MET cc_start: 0.8789 (mpp) cc_final: 0.8360 (mpp) REVERT: B 605 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9128 (pp) REVERT: B 608 MET cc_start: 0.9474 (ptp) cc_final: 0.9089 (ptp) REVERT: C 46 MET cc_start: 0.8003 (mtt) cc_final: 0.6514 (tpt) REVERT: C 163 PHE cc_start: 0.7018 (t80) cc_final: 0.6384 (t80) REVERT: D 46 MET cc_start: 0.8098 (tpt) cc_final: 0.7820 (mtt) REVERT: D 117 LEU cc_start: 0.8356 (tp) cc_final: 0.8049 (tt) REVERT: D 163 PHE cc_start: 0.7055 (t80) cc_final: 0.6366 (t80) REVERT: F 84 MET cc_start: 0.7086 (ttt) cc_final: 0.6618 (tmm) REVERT: F 678 MET cc_start: 0.8810 (ppp) cc_final: 0.8304 (ppp) outliers start: 92 outliers final: 66 residues processed: 207 average time/residue: 0.3914 time to fit residues: 144.0818 Evaluate side-chains 202 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 135 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 252 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 82 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 268 optimal weight: 9.9990 chunk 287 optimal weight: 0.0980 chunk 208 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN F 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35460 Z= 0.234 Angle : 0.636 14.510 47952 Z= 0.290 Chirality : 0.044 0.193 5376 Planarity : 0.004 0.086 6300 Dihedral : 6.335 69.048 4914 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.83 % Favored : 95.90 % Rotamer: Outliers : 2.27 % Allowed : 15.15 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.77 (0.13), residues: 4386 helix: -0.11 (0.13), residues: 1680 sheet: -0.02 (0.21), residues: 642 loop : -0.92 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.003 0.001 HIS F 340 PHE 0.017 0.001 PHE E 516 TYR 0.008 0.001 TYR E 755 ARG 0.004 0.000 ARG E 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 133 time to evaluate : 5.318 Fit side-chains revert: symmetry clash REVERT: A 275 MET cc_start: 0.8828 (mpp) cc_final: 0.8449 (mpp) REVERT: B 46 MET cc_start: 0.7720 (mpp) cc_final: 0.5954 (tpp) REVERT: B 605 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9142 (pp) REVERT: B 608 MET cc_start: 0.9465 (ptp) cc_final: 0.9087 (ptp) REVERT: C 46 MET cc_start: 0.8032 (mtt) cc_final: 0.6544 (tpt) REVERT: C 163 PHE cc_start: 0.7134 (t80) cc_final: 0.6480 (t80) REVERT: D 46 MET cc_start: 0.7972 (tpt) cc_final: 0.7720 (mtt) REVERT: D 117 LEU cc_start: 0.8367 (tp) cc_final: 0.8059 (tt) REVERT: D 163 PHE cc_start: 0.6931 (t80) cc_final: 0.6238 (t80) REVERT: E 46 MET cc_start: 0.7353 (mpp) cc_final: 0.5435 (tpp) REVERT: E 608 MET cc_start: 0.9459 (ptp) cc_final: 0.9079 (ptp) REVERT: F 46 MET cc_start: 0.7670 (mpp) cc_final: 0.5946 (tpp) REVERT: F 84 MET cc_start: 0.7051 (ttt) cc_final: 0.6552 (tmm) REVERT: F 678 MET cc_start: 0.8760 (ppp) cc_final: 0.8512 (ppp) outliers start: 85 outliers final: 76 residues processed: 192 average time/residue: 0.3920 time to fit residues: 134.5842 Evaluate side-chains 210 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 133 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 393 optimal weight: 0.9980 chunk 236 optimal weight: 50.0000 chunk 171 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 372 optimal weight: 30.0000 chunk 392 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35460 Z= 0.237 Angle : 0.640 15.157 47952 Z= 0.290 Chirality : 0.045 0.259 5376 Planarity : 0.004 0.082 6300 Dihedral : 6.307 68.590 4914 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.20 % Favored : 95.53 % Rotamer: Outliers : 2.61 % Allowed : 14.96 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.75 (0.13), residues: 4386 helix: -0.06 (0.13), residues: 1638 sheet: -0.03 (0.21), residues: 642 loop : -0.92 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.004 0.001 HIS A 384 PHE 0.016 0.001 PHE E 516 TYR 0.008 0.001 TYR D 755 ARG 0.004 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 132 time to evaluate : 4.285 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.8166 (tpt) cc_final: 0.7881 (mtt) REVERT: A 275 MET cc_start: 0.8818 (mpp) cc_final: 0.8392 (mpp) REVERT: B 605 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9188 (pp) REVERT: B 608 MET cc_start: 0.9461 (ptp) cc_final: 0.9097 (ptp) REVERT: C 46 MET cc_start: 0.7955 (mtt) cc_final: 0.6422 (tpt) REVERT: C 678 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8258 (ptp) REVERT: D 46 MET cc_start: 0.8062 (tpt) cc_final: 0.7798 (mtt) REVERT: D 117 LEU cc_start: 0.8455 (tp) cc_final: 0.8150 (tt) REVERT: D 163 PHE cc_start: 0.6882 (t80) cc_final: 0.6186 (t80) REVERT: D 449 MET cc_start: 0.8555 (tpp) cc_final: 0.8083 (tpp) REVERT: E 608 MET cc_start: 0.9444 (ptp) cc_final: 0.9087 (ptp) REVERT: F 84 MET cc_start: 0.7044 (ttt) cc_final: 0.6547 (tmm) REVERT: F 678 MET cc_start: 0.8745 (ppp) cc_final: 0.8494 (ppp) outliers start: 98 outliers final: 83 residues processed: 202 average time/residue: 0.4165 time to fit residues: 148.2375 Evaluate side-chains 215 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 130 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 289 optimal weight: 30.0000 chunk 436 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35460 Z= 0.211 Angle : 0.643 15.634 47952 Z= 0.289 Chirality : 0.045 0.268 5376 Planarity : 0.004 0.084 6300 Dihedral : 6.281 68.591 4914 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.08 % Favored : 95.65 % Rotamer: Outliers : 2.16 % Allowed : 15.44 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4386 helix: -0.03 (0.13), residues: 1638 sheet: -0.00 (0.21), residues: 642 loop : -0.90 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 551 HIS 0.003 0.001 HIS F 340 PHE 0.014 0.001 PHE B 516 TYR 0.008 0.001 TYR D 755 ARG 0.003 0.000 ARG F 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 130 time to evaluate : 4.182 Fit side-chains REVERT: A 46 MET cc_start: 0.8169 (tpt) cc_final: 0.7879 (mtt) REVERT: A 275 MET cc_start: 0.8782 (mpp) cc_final: 0.8377 (mpp) REVERT: B 46 MET cc_start: 0.7472 (mpp) cc_final: 0.5715 (mmm) REVERT: B 605 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9181 (pp) REVERT: B 608 MET cc_start: 0.9451 (ptp) cc_final: 0.9091 (ptp) REVERT: C 46 MET cc_start: 0.7706 (mtt) cc_final: 0.6230 (tpt) REVERT: C 678 MET cc_start: 0.8502 (ptp) cc_final: 0.8243 (ptp) REVERT: D 46 MET cc_start: 0.8069 (tpt) cc_final: 0.7808 (mtt) REVERT: D 117 LEU cc_start: 0.8456 (tp) cc_final: 0.8178 (tt) REVERT: D 449 MET cc_start: 0.8439 (tpp) cc_final: 0.7991 (tpp) REVERT: E 608 MET cc_start: 0.9409 (ptp) cc_final: 0.9115 (ptp) REVERT: F 84 MET cc_start: 0.7038 (ttt) cc_final: 0.6545 (tmm) REVERT: F 678 MET cc_start: 0.8728 (ppp) cc_final: 0.8471 (ppp) outliers start: 81 outliers final: 78 residues processed: 185 average time/residue: 0.4079 time to fit residues: 134.1060 Evaluate side-chains 208 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 129 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 40.0000 chunk 370 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 348 optimal weight: 4.9990 chunk 145 optimal weight: 40.0000 chunk 357 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN F 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.087312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058534 restraints weight = 127042.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059566 restraints weight = 80772.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060069 restraints weight = 62491.294| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 35460 Z= 0.258 Angle : 0.733 59.199 47952 Z= 0.362 Chirality : 0.045 0.327 5376 Planarity : 0.004 0.084 6300 Dihedral : 6.283 68.551 4914 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 2.32 % Allowed : 15.57 % Favored : 82.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4386 helix: -0.04 (0.13), residues: 1638 sheet: 0.00 (0.21), residues: 642 loop : -0.90 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 551 HIS 0.003 0.001 HIS F 340 PHE 0.028 0.001 PHE D 163 TYR 0.007 0.001 TYR D 755 ARG 0.003 0.000 ARG F 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4734.02 seconds wall clock time: 89 minutes 29.48 seconds (5369.48 seconds total)