Starting phenix.real_space_refine on Sat Mar 23 04:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcx_31899/03_2024/7vcx_31899_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 198 5.16 5 C 22146 2.51 5 N 6276 2.21 5 O 6822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 210": "NH1" <-> "NH2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F ARG 708": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35490 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "B" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "C" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "D" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "E" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "F" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 19.07, per 1000 atoms: 0.54 Number of scatterers: 35490 At special positions: 0 Unit cell: (182.52, 173.88, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 198 16.00 P 36 15.00 Mg 12 11.99 O 6822 8.00 N 6276 7.00 C 22146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.73 Conformation dependent library (CDL) restraints added in 7.0 seconds 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 30 sheets defined 42.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.24 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'A' and resid 252 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 337 removed outlier: 4.959A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN A 337 " --> pdb=" O ASP A 333 " (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 removed outlier: 3.663A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 429 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 449 through 455 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: 3.675A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 595 through 609 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.121A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.959A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN B 337 " --> pdb=" O ASP B 333 " (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 removed outlier: 3.663A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 429 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 449 through 455 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: 3.675A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 555 through 568 Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 4.120A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'C' and resid 252 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 337 removed outlier: 4.958A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN C 337 " --> pdb=" O ASP C 333 " (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 removed outlier: 3.663A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 429 Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 449 through 455 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: 3.675A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 579 through 585 Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 removed outlier: 4.121A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'D' and resid 252 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 337 removed outlier: 4.959A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN D 337 " --> pdb=" O ASP D 333 " (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 removed outlier: 3.663A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 429 Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 449 through 455 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: 3.675A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 549 Processing helix chain 'D' and resid 555 through 568 Processing helix chain 'D' and resid 579 through 585 Processing helix chain 'D' and resid 595 through 609 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.121A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'E' and resid 252 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 337 removed outlier: 4.959A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (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 removed outlier: 3.663A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 429 Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 449 through 455 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: 3.675A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 Processing helix chain 'E' and resid 555 through 568 Processing helix chain 'E' and resid 579 through 585 Processing helix chain 'E' and resid 595 through 609 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.120A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' 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 210 through 225 removed outlier: 4.929A 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 233 Processing helix chain 'F' and resid 252 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 337 removed outlier: 4.958A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN F 337 " --> pdb=" O ASP F 333 " (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 removed outlier: 3.663A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 429 Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 449 through 455 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: 3.675A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (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 524 through 534 removed outlier: 3.951A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 549 Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 579 through 585 Processing helix chain 'F' and resid 595 through 609 Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.035A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 761 removed outlier: 4.121A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.927A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 7.200A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 642 through 645 removed outlier: 8.130A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 645 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR A 517 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.927A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 7.199A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 642 through 645 removed outlier: 8.130A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 645 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 517 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.926A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 7.200A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 642 through 645 removed outlier: 8.129A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE C 645 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR C 517 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 81 through 83 removed outlier: 7.927A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 7.200A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 642 through 645 removed outlier: 8.130A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE D 645 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR D 517 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.927A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 7.199A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 642 through 645 removed outlier: 8.130A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.926A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 181 through 183 removed outlier: 7.200A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.698A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 642 through 645 removed outlier: 8.129A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE F 645 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR F 517 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1200 hydrogen bonds defined for protein. 3564 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: 12.77 Time building geometry restraints manager: 14.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12716 1.36 - 1.50: 11162 1.50 - 1.65: 11882 1.65 - 1.79: 210 1.79 - 1.94: 102 Bond restraints: 36072 Sorted by residual: bond pdb=" CG1 ILE B 380 " pdb=" CD1 ILE B 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE E 380 " pdb=" CD1 ILE E 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE C 380 " pdb=" CD1 ILE C 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE F 380 " pdb=" CD1 ILE F 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CB GLN D 327 " pdb=" CG GLN D 327 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.44e+00 ... (remaining 36067 not shown) Histogram of bond angle deviations from ideal: 97.02 - 105.00: 964 105.00 - 112.99: 19496 112.99 - 120.97: 18488 120.97 - 128.95: 9646 128.95 - 136.93: 192 Bond angle restraints: 48786 Sorted by residual: angle pdb=" CB ARG F 358 " pdb=" CG ARG F 358 " pdb=" CD ARG F 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG C 358 " pdb=" CG ARG C 358 " pdb=" CD ARG C 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG E 358 " pdb=" CG ARG E 358 " pdb=" CD ARG E 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG B 358 " pdb=" CG ARG B 358 " pdb=" CD ARG B 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG D 358 " pdb=" CG ARG D 358 " pdb=" CD ARG D 358 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 ... (remaining 48781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.19: 19664 11.19 - 22.37: 2114 22.37 - 33.56: 476 33.56 - 44.74: 132 44.74 - 55.93: 78 Dihedral angle restraints: 22464 sinusoidal: 9570 harmonic: 12894 Sorted by residual: dihedral pdb=" CA MET C 550 " pdb=" C MET C 550 " pdb=" N TRP C 551 " pdb=" CA TRP C 551 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA MET F 550 " pdb=" C MET F 550 " pdb=" N TRP F 551 " pdb=" CA TRP F 551 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA MET E 550 " pdb=" C MET E 550 " pdb=" N TRP E 551 " pdb=" CA TRP E 551 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 22461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2694 0.044 - 0.088: 1762 0.088 - 0.132: 708 0.132 - 0.176: 266 0.176 - 0.219: 48 Chirality restraints: 5478 Sorted by residual: chirality pdb=" PA AGS F 901 " pdb=" O2A AGS F 901 " pdb=" O3A AGS F 901 " pdb=" O5' AGS F 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" PA AGS C 901 " pdb=" O2A AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O5' AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" PA AGS D 901 " pdb=" O2A AGS D 901 " pdb=" O3A AGS D 901 " pdb=" O5' AGS D 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5475 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 516 " 0.023 2.00e-02 2.50e+03 2.03e-02 7.21e+00 pdb=" CG PHE F 516 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE F 516 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 516 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 516 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 516 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 516 " -0.023 2.00e-02 2.50e+03 2.03e-02 7.21e+00 pdb=" CG PHE C 516 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 516 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 516 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 516 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 516 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 105 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO C 106 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.037 5.00e-02 4.00e+02 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 372 2.63 - 3.20: 29716 3.20 - 3.77: 49188 3.77 - 4.33: 69244 4.33 - 4.90: 115990 Nonbonded interactions: 264510 Sorted by model distance: nonbonded pdb=" O1B AGS E 903 " pdb="MG MG E 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS B 903 " pdb="MG MG B 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS F 903 " pdb="MG MG F 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS C 903 " pdb="MG MG C 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS D 903 " pdb="MG MG D 904 " model vdw 2.065 2.170 ... (remaining 264505 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 individual isotropic 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.160 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 92.720 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.016 0.114 36072 Z= 1.039 Angle : 1.216 11.281 48786 Z= 0.663 Chirality : 0.067 0.219 5478 Planarity : 0.009 0.067 6420 Dihedral : 10.491 55.929 14100 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.10), residues: 4452 helix: -2.31 (0.09), residues: 1992 sheet: -1.21 (0.16), residues: 666 loop : -2.48 (0.12), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP D 454 HIS 0.012 0.003 HIS E 406 PHE 0.047 0.005 PHE F 516 TYR 0.036 0.007 TYR C 203 ARG 0.015 0.002 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6604 (mtp) cc_final: 0.6281 (mtp) REVERT: A 307 ASP cc_start: 0.8420 (p0) cc_final: 0.8194 (p0) REVERT: A 344 MET cc_start: 0.8678 (mtp) cc_final: 0.8464 (mtm) REVERT: B 46 MET cc_start: 0.6564 (mtp) cc_final: 0.6295 (mtp) REVERT: B 332 MET cc_start: 0.8631 (mmm) cc_final: 0.8412 (mmm) REVERT: C 46 MET cc_start: 0.6466 (mtp) cc_final: 0.6208 (mtp) REVERT: D 46 MET cc_start: 0.6588 (mtp) cc_final: 0.6263 (mtp) REVERT: D 307 ASP cc_start: 0.8422 (p0) cc_final: 0.8196 (p0) REVERT: D 344 MET cc_start: 0.8675 (mtp) cc_final: 0.8462 (mtm) REVERT: E 46 MET cc_start: 0.6559 (mtp) cc_final: 0.6287 (mtp) REVERT: E 332 MET cc_start: 0.8609 (mmm) cc_final: 0.8391 (mmm) REVERT: F 46 MET cc_start: 0.6473 (mtp) cc_final: 0.6213 (mtp) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.6141 time to fit residues: 452.1964 Evaluate side-chains 266 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 348 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 103 GLN ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 90 ASN B 103 GLN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 558 ASN C 90 ASN C 103 GLN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 558 ASN D 90 ASN D 103 GLN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 90 ASN E 103 GLN ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN E 558 ASN F 90 ASN F 103 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 558 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36072 Z= 0.168 Angle : 0.556 5.886 48786 Z= 0.288 Chirality : 0.044 0.130 5478 Planarity : 0.006 0.050 6420 Dihedral : 8.213 58.811 5112 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.94 % Allowed : 4.14 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.55 (0.12), residues: 4452 helix: -0.37 (0.11), residues: 2004 sheet: -0.43 (0.18), residues: 612 loop : -1.92 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.003 0.001 HIS F 115 PHE 0.014 0.001 PHE A 516 TYR 0.010 0.001 TYR F 244 ARG 0.007 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 332 time to evaluate : 4.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6615 (mtp) cc_final: 0.6381 (mtp) REVERT: A 344 MET cc_start: 0.8630 (mtp) cc_final: 0.8422 (mtm) REVERT: A 608 MET cc_start: 0.8680 (mtt) cc_final: 0.8407 (mtp) REVERT: C 46 MET cc_start: 0.6458 (mtp) cc_final: 0.6253 (mtp) REVERT: D 46 MET cc_start: 0.6608 (mtp) cc_final: 0.6374 (mtp) REVERT: D 344 MET cc_start: 0.8628 (mtp) cc_final: 0.8423 (mtm) REVERT: D 608 MET cc_start: 0.8685 (mtt) cc_final: 0.8409 (mtp) REVERT: F 46 MET cc_start: 0.6461 (mtp) cc_final: 0.6257 (mtp) outliers start: 36 outliers final: 18 residues processed: 360 average time/residue: 0.4906 time to fit residues: 283.5138 Evaluate side-chains 278 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 260 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 335 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 403 optimal weight: 1.9990 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 0.0470 chunk 400 optimal weight: 4.9990 chunk 137 optimal weight: 0.0370 chunk 324 optimal weight: 4.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36072 Z= 0.207 Angle : 0.520 5.855 48786 Z= 0.264 Chirality : 0.044 0.131 5478 Planarity : 0.005 0.043 6420 Dihedral : 7.551 58.756 5112 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.05 % Allowed : 5.77 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.12), residues: 4452 helix: 0.37 (0.12), residues: 2028 sheet: -0.11 (0.19), residues: 618 loop : -1.56 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 454 HIS 0.002 0.001 HIS C 384 PHE 0.012 0.001 PHE C 152 TYR 0.011 0.002 TYR F 244 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 4.149 Fit side-chains REVERT: A 344 MET cc_start: 0.8602 (mtp) cc_final: 0.8342 (mtm) REVERT: B 46 MET cc_start: 0.6886 (ttm) cc_final: 0.6069 (mtp) REVERT: D 344 MET cc_start: 0.8600 (mtp) cc_final: 0.8343 (mtm) REVERT: E 46 MET cc_start: 0.6887 (ttm) cc_final: 0.6064 (mtp) outliers start: 40 outliers final: 22 residues processed: 290 average time/residue: 0.4385 time to fit residues: 212.1104 Evaluate side-chains 276 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 1.9990 chunk 429 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 384 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36072 Z= 0.178 Angle : 0.487 6.041 48786 Z= 0.246 Chirality : 0.043 0.126 5478 Planarity : 0.004 0.040 6420 Dihedral : 7.167 58.080 5112 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.79 % Allowed : 6.71 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.16 (0.13), residues: 4452 helix: 0.84 (0.12), residues: 2040 sheet: 0.15 (0.19), residues: 606 loop : -1.27 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.002 0.001 HIS F 384 PHE 0.012 0.001 PHE C 152 TYR 0.010 0.001 TYR F 244 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 268 time to evaluate : 3.801 Fit side-chains REVERT: B 46 MET cc_start: 0.6938 (ttm) cc_final: 0.6053 (mtp) REVERT: E 46 MET cc_start: 0.6937 (ttm) cc_final: 0.6047 (mtp) outliers start: 30 outliers final: 20 residues processed: 292 average time/residue: 0.4634 time to fit residues: 221.4711 Evaluate side-chains 270 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 385 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36072 Z= 0.330 Angle : 0.567 6.393 48786 Z= 0.285 Chirality : 0.045 0.137 5478 Planarity : 0.005 0.042 6420 Dihedral : 7.208 58.820 5112 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.21 % Allowed : 6.66 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.17 (0.13), residues: 4452 helix: 0.84 (0.12), residues: 2046 sheet: -0.07 (0.19), residues: 600 loop : -1.19 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 476 HIS 0.004 0.001 HIS D 384 PHE 0.019 0.002 PHE A 267 TYR 0.020 0.002 TYR E 495 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 4.864 Fit side-chains REVERT: A 344 MET cc_start: 0.8708 (mtp) cc_final: 0.8406 (mtm) REVERT: B 46 MET cc_start: 0.6960 (ttm) cc_final: 0.6052 (mtp) REVERT: E 46 MET cc_start: 0.6960 (ttm) cc_final: 0.6047 (mtp) outliers start: 46 outliers final: 30 residues processed: 284 average time/residue: 0.4891 time to fit residues: 231.8774 Evaluate side-chains 276 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 7.9990 chunk 386 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 429 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36072 Z= 0.246 Angle : 0.518 6.369 48786 Z= 0.261 Chirality : 0.044 0.131 5478 Planarity : 0.004 0.043 6420 Dihedral : 7.050 58.019 5112 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.34 % Allowed : 7.13 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.03 (0.13), residues: 4452 helix: 1.01 (0.12), residues: 2052 sheet: 0.01 (0.20), residues: 600 loop : -1.10 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.002 0.001 HIS F 384 PHE 0.012 0.001 PHE A 230 TYR 0.012 0.001 TYR C 244 ARG 0.003 0.000 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 3.849 Fit side-chains REVERT: A 344 MET cc_start: 0.8657 (mtp) cc_final: 0.8355 (mtm) REVERT: B 46 MET cc_start: 0.6997 (ttm) cc_final: 0.6057 (mtp) REVERT: C 46 MET cc_start: 0.6683 (ttm) cc_final: 0.5970 (mtp) REVERT: D 344 MET cc_start: 0.8654 (mtp) cc_final: 0.8357 (mtm) REVERT: E 46 MET cc_start: 0.6997 (ttm) cc_final: 0.6048 (mtp) REVERT: E 94 VAL cc_start: 0.8514 (t) cc_final: 0.8313 (t) REVERT: F 46 MET cc_start: 0.6686 (ttm) cc_final: 0.5972 (mtp) outliers start: 51 outliers final: 31 residues processed: 290 average time/residue: 0.4356 time to fit residues: 214.0718 Evaluate side-chains 272 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.0670 chunk 48 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 313 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 239 optimal weight: 0.0050 chunk 427 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 overall best weight: 0.7334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 558 ASN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36072 Z= 0.133 Angle : 0.463 7.815 48786 Z= 0.231 Chirality : 0.042 0.129 5478 Planarity : 0.004 0.042 6420 Dihedral : 6.688 57.851 5112 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.71 % Allowed : 8.07 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.42 (0.13), residues: 4452 helix: 1.37 (0.12), residues: 2016 sheet: 0.36 (0.20), residues: 606 loop : -0.97 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 454 HIS 0.002 0.000 HIS E 317 PHE 0.010 0.001 PHE F 152 TYR 0.007 0.001 TYR F 244 ARG 0.002 0.000 ARG E 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 4.102 Fit side-chains REVERT: A 344 MET cc_start: 0.8582 (mtp) cc_final: 0.8303 (mtm) REVERT: B 46 MET cc_start: 0.7117 (ttm) cc_final: 0.6185 (mtp) REVERT: C 46 MET cc_start: 0.6794 (ttm) cc_final: 0.6036 (mtp) REVERT: C 94 VAL cc_start: 0.8587 (t) cc_final: 0.8318 (p) REVERT: C 668 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8414 (mmtp) REVERT: D 344 MET cc_start: 0.8582 (mtp) cc_final: 0.8300 (mtm) REVERT: E 46 MET cc_start: 0.7113 (ttm) cc_final: 0.6176 (mtp) REVERT: F 46 MET cc_start: 0.6798 (ttm) cc_final: 0.6039 (mtp) REVERT: F 94 VAL cc_start: 0.8586 (t) cc_final: 0.8317 (p) REVERT: F 668 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8404 (mmtp) outliers start: 27 outliers final: 18 residues processed: 276 average time/residue: 0.4568 time to fit residues: 208.8387 Evaluate side-chains 262 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36072 Z= 0.285 Angle : 0.533 10.164 48786 Z= 0.264 Chirality : 0.044 0.131 5478 Planarity : 0.004 0.041 6420 Dihedral : 6.836 57.603 5112 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.86 % Allowed : 7.94 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.31 (0.13), residues: 4452 helix: 1.20 (0.12), residues: 2052 sheet: 0.26 (0.20), residues: 600 loop : -0.95 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 476 HIS 0.004 0.001 HIS C 499 PHE 0.014 0.002 PHE E 516 TYR 0.014 0.002 TYR E 495 ARG 0.007 0.000 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 4.455 Fit side-chains REVERT: B 46 MET cc_start: 0.7116 (ttm) cc_final: 0.6157 (mtp) REVERT: B 484 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: C 46 MET cc_start: 0.6814 (ttm) cc_final: 0.6044 (mtp) REVERT: E 46 MET cc_start: 0.7112 (ttm) cc_final: 0.6149 (mtp) REVERT: E 484 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: F 46 MET cc_start: 0.6815 (ttm) cc_final: 0.6049 (mtp) outliers start: 33 outliers final: 29 residues processed: 264 average time/residue: 0.4364 time to fit residues: 197.0749 Evaluate side-chains 269 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 1.9990 chunk 409 optimal weight: 0.9980 chunk 374 optimal weight: 0.5980 chunk 398 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 360 optimal weight: 0.6980 chunk 377 optimal weight: 5.9990 chunk 397 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36072 Z= 0.140 Angle : 0.475 10.574 48786 Z= 0.234 Chirality : 0.042 0.127 5478 Planarity : 0.004 0.042 6420 Dihedral : 6.620 57.997 5112 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.66 % Allowed : 8.31 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.58 (0.13), residues: 4452 helix: 1.46 (0.12), residues: 2016 sheet: 0.52 (0.21), residues: 606 loop : -0.88 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 454 HIS 0.002 0.000 HIS C 499 PHE 0.010 0.001 PHE C 152 TYR 0.008 0.001 TYR F 244 ARG 0.003 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 3.920 Fit side-chains REVERT: B 46 MET cc_start: 0.7117 (ttm) cc_final: 0.6182 (mtp) REVERT: C 46 MET cc_start: 0.6786 (ttm) cc_final: 0.5996 (mtp) REVERT: C 668 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8390 (mmtp) REVERT: E 46 MET cc_start: 0.7115 (ttm) cc_final: 0.6178 (mtp) REVERT: F 46 MET cc_start: 0.6788 (ttm) cc_final: 0.6000 (mtp) REVERT: F 668 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8382 (mmtp) outliers start: 25 outliers final: 22 residues processed: 260 average time/residue: 0.4294 time to fit residues: 190.0767 Evaluate side-chains 256 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 200 optimal weight: 0.0050 chunk 293 optimal weight: 9.9990 chunk 442 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36072 Z= 0.254 Angle : 0.522 12.297 48786 Z= 0.256 Chirality : 0.044 0.130 5478 Planarity : 0.004 0.041 6420 Dihedral : 6.716 57.899 5112 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.71 % Allowed : 8.28 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.49 (0.13), residues: 4452 helix: 1.38 (0.12), residues: 2010 sheet: 0.45 (0.21), residues: 600 loop : -0.89 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 476 HIS 0.004 0.001 HIS C 499 PHE 0.012 0.001 PHE A 516 TYR 0.012 0.001 TYR B 495 ARG 0.004 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 4.057 Fit side-chains REVERT: B 46 MET cc_start: 0.7120 (ttm) cc_final: 0.6166 (mtp) REVERT: C 46 MET cc_start: 0.6931 (ttm) cc_final: 0.6281 (mtp) REVERT: E 46 MET cc_start: 0.7121 (ttm) cc_final: 0.6161 (mtp) REVERT: F 46 MET cc_start: 0.6934 (ttm) cc_final: 0.6286 (mtp) outliers start: 27 outliers final: 26 residues processed: 258 average time/residue: 0.4239 time to fit residues: 187.7801 Evaluate side-chains 257 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 231 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 3.9990 chunk 375 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 324 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 97 optimal weight: 3.9990 chunk 352 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122660 restraints weight = 44019.535| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.46 r_work: 0.3095 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36072 Z= 0.162 Angle : 0.483 12.112 48786 Z= 0.236 Chirality : 0.042 0.128 5478 Planarity : 0.004 0.042 6420 Dihedral : 6.581 58.047 5112 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.60 % Allowed : 8.49 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.69 (0.13), residues: 4452 helix: 1.51 (0.12), residues: 2010 sheet: 0.69 (0.21), residues: 600 loop : -0.80 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.002 0.000 HIS F 499 PHE 0.010 0.001 PHE C 152 TYR 0.009 0.001 TYR F 244 ARG 0.003 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6340.01 seconds wall clock time: 115 minutes 14.73 seconds (6914.73 seconds total)