Starting phenix.real_space_refine on Sat Mar 23 05:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vct_31895/03_2024/7vct_31895_updated.pdb" } resolution = 3.21 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 30 5.49 5 Mg 6 5.21 5 S 192 5.16 5 C 22296 2.51 5 N 6312 2.21 5 O 6858 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 ARG 225": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F ARG 708": "NH1" <-> "NH2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F ARG 741": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35694 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "B" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "C" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "D" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "E" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "F" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.39, per 1000 atoms: 0.49 Number of scatterers: 35694 At special positions: 0 Unit cell: (178.2, 176.04, 103.68, 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 192 16.00 P 30 15.00 Mg 6 11.99 O 6858 8.00 N 6312 7.00 C 22296 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 6.3 seconds 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 36 sheets defined 40.1% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.41 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) 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 334 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: 3.519A 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 425 Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 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 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 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.740A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.420A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) 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 334 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: 3.518A 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 425 Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 458 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 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 Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.740A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 652 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.421A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) 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 334 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: 3.519A 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 425 Processing helix chain 'C' and resid 429 through 432 No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 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 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 Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.741A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 652 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.421A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) 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 334 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: 3.519A 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 425 Processing helix chain 'D' and resid 429 through 432 No H-bonds generated for 'chain 'D' and resid 429 through 432' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 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 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 Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.740A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 652 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.420A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) 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 334 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: 3.518A 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 425 Processing helix chain 'E' and resid 429 through 432 No H-bonds generated for 'chain 'E' and resid 429 through 432' Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 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 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 Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.740A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 652 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.421A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 762 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' 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: 5.153A 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 231 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.773A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) 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 334 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: 3.519A 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 425 Processing helix chain 'F' and resid 429 through 432 No H-bonds generated for 'chain 'F' and resid 429 through 432' Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 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 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 Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.741A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 removed outlier: 3.682A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 652 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 removed outlier: 3.834A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.421A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.525A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.932A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.459A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.525A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.933A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.460A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.526A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.933A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 368 removed outlier: 6.459A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 81 through 83 removed outlier: 7.525A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.932A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= W, first strand: chain 'D' and resid 365 through 368 removed outlier: 6.459A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.525A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.933A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'E' and resid 365 through 368 removed outlier: 6.460A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.526A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.151A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.933A pdb=" N VAL F 116 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AI, first strand: chain 'F' and resid 365 through 368 removed outlier: 6.459A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.836A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3366 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: 14.51 Time building geometry restraints manager: 13.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 12410 1.37 - 1.51: 10768 1.51 - 1.66: 12810 1.66 - 1.80: 246 1.80 - 1.95: 60 Bond restraints: 36294 Sorted by residual: bond pdb=" C4 ADP B 903 " pdb=" C5 ADP B 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP C 903 " pdb=" C5 ADP C 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 903 " pdb=" C5 ADP E 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 903 " pdb=" C5 ADP A 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP D 903 " pdb=" C5 ADP D 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 36289 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.78: 814 104.78 - 112.09: 17698 112.09 - 119.39: 12412 119.39 - 126.69: 17729 126.69 - 133.99: 433 Bond angle restraints: 49086 Sorted by residual: angle pdb=" N ASP A 592 " pdb=" CA ASP A 592 " pdb=" C ASP A 592 " ideal model delta sigma weight residual 111.03 105.82 5.21 1.11e+00 8.12e-01 2.20e+01 angle pdb=" N ASP D 592 " pdb=" CA ASP D 592 " pdb=" C ASP D 592 " ideal model delta sigma weight residual 111.03 105.82 5.21 1.11e+00 8.12e-01 2.20e+01 angle pdb=" N ASP C 592 " pdb=" CA ASP C 592 " pdb=" C ASP C 592 " ideal model delta sigma weight residual 111.03 105.83 5.20 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ASP F 592 " pdb=" CA ASP F 592 " pdb=" C ASP F 592 " ideal model delta sigma weight residual 111.03 105.83 5.20 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ASP B 592 " pdb=" CA ASP B 592 " pdb=" C ASP B 592 " ideal model delta sigma weight residual 111.03 105.85 5.18 1.11e+00 8.12e-01 2.18e+01 ... (remaining 49081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 22138 24.70 - 49.39: 351 49.39 - 74.09: 36 74.09 - 98.78: 6 98.78 - 123.48: 11 Dihedral angle restraints: 22542 sinusoidal: 9564 harmonic: 12978 Sorted by residual: dihedral pdb=" O1B ADP B 903 " pdb=" O3A ADP B 903 " pdb=" PB ADP B 903 " pdb=" PA ADP B 903 " ideal model delta sinusoidal sigma weight residual 300.00 176.52 123.48 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" O1B ADP E 903 " pdb=" O3A ADP E 903 " pdb=" PB ADP E 903 " pdb=" PA ADP E 903 " ideal model delta sinusoidal sigma weight residual 300.00 176.95 123.05 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' ADP C 903 " pdb=" O5' ADP C 903 " pdb=" PA ADP C 903 " pdb=" O2A ADP C 903 " ideal model delta sinusoidal sigma weight residual -60.00 62.18 -122.18 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 22539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4121 0.058 - 0.116: 1165 0.116 - 0.174: 190 0.174 - 0.232: 14 0.232 - 0.290: 6 Chirality restraints: 5496 Sorted by residual: chirality pdb=" C3' ADP C 903 " pdb=" C2' ADP C 903 " pdb=" C4' ADP C 903 " pdb=" O3' ADP C 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ADP E 903 " pdb=" C2' ADP E 903 " pdb=" C4' ADP E 903 " pdb=" O3' ADP E 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ADP D 903 " pdb=" C2' ADP D 903 " pdb=" C4' ADP D 903 " pdb=" O3' ADP D 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 5493 not shown) Planarity restraints: 6474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO C 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 544 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO F 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 545 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 544 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO D 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " -0.035 5.00e-02 4.00e+02 ... (remaining 6471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 633 2.69 - 3.24: 31567 3.24 - 3.79: 49783 3.79 - 4.35: 68089 4.35 - 4.90: 112935 Nonbonded interactions: 263007 Sorted by model distance: nonbonded pdb=" O2G AGS E 901 " pdb="MG MG E 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS B 901 " pdb="MG MG B 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS D 901 " pdb="MG MG D 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS C 901 " pdb="MG MG C 902 " model vdw 2.132 2.170 ... (remaining 263002 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.110 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 89.560 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.007 0.109 36294 Z= 0.441 Angle : 0.941 12.909 49086 Z= 0.518 Chirality : 0.054 0.290 5496 Planarity : 0.008 0.063 6474 Dihedral : 9.934 123.478 14130 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -3.08 (0.10), residues: 4494 helix: -2.41 (0.09), residues: 1776 sheet: -0.07 (0.20), residues: 624 loop : -2.29 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 454 HIS 0.005 0.001 HIS A 340 PHE 0.041 0.003 PHE C 516 TYR 0.024 0.003 TYR D 755 ARG 0.014 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7010 (mttp) cc_final: 0.6753 (ttpp) REVERT: A 443 ASN cc_start: 0.7163 (m-40) cc_final: 0.6863 (m-40) REVERT: A 449 MET cc_start: 0.8007 (tpt) cc_final: 0.7639 (tpt) REVERT: A 457 SER cc_start: 0.8669 (t) cc_final: 0.8306 (p) REVERT: A 678 MET cc_start: 0.6340 (tpt) cc_final: 0.6102 (tpt) REVERT: A 742 PHE cc_start: 0.7442 (m-80) cc_final: 0.6800 (m-10) REVERT: A 752 ILE cc_start: 0.9000 (mt) cc_final: 0.8761 (mm) REVERT: B 443 ASN cc_start: 0.7199 (m-40) cc_final: 0.6723 (m-40) REVERT: B 449 MET cc_start: 0.7920 (tpt) cc_final: 0.7428 (tpp) REVERT: B 457 SER cc_start: 0.8516 (t) cc_final: 0.8209 (p) REVERT: C 62 LYS cc_start: 0.7043 (mttp) cc_final: 0.6757 (ttpp) REVERT: C 443 ASN cc_start: 0.7272 (m-40) cc_final: 0.6940 (m-40) REVERT: C 457 SER cc_start: 0.8585 (t) cc_final: 0.8274 (p) REVERT: C 550 MET cc_start: 0.8766 (mtt) cc_final: 0.8564 (mtm) REVERT: C 678 MET cc_start: 0.6483 (tpt) cc_final: 0.6080 (tpt) REVERT: D 62 LYS cc_start: 0.7011 (mttp) cc_final: 0.6755 (ttpp) REVERT: D 443 ASN cc_start: 0.7163 (m-40) cc_final: 0.6862 (m-40) REVERT: D 449 MET cc_start: 0.8005 (tpt) cc_final: 0.7645 (tpt) REVERT: D 457 SER cc_start: 0.8651 (t) cc_final: 0.8308 (p) REVERT: D 678 MET cc_start: 0.6318 (tpt) cc_final: 0.6086 (tpt) REVERT: D 742 PHE cc_start: 0.7447 (m-80) cc_final: 0.6807 (m-10) REVERT: D 752 ILE cc_start: 0.9001 (mt) cc_final: 0.8756 (mm) REVERT: E 443 ASN cc_start: 0.7198 (m-40) cc_final: 0.6721 (m-40) REVERT: E 449 MET cc_start: 0.7919 (tpt) cc_final: 0.7422 (tpp) REVERT: E 457 SER cc_start: 0.8509 (t) cc_final: 0.8197 (p) REVERT: F 62 LYS cc_start: 0.7043 (mttp) cc_final: 0.6761 (ttpp) REVERT: F 443 ASN cc_start: 0.7274 (m-40) cc_final: 0.6937 (m-40) REVERT: F 457 SER cc_start: 0.8591 (t) cc_final: 0.8272 (p) REVERT: F 678 MET cc_start: 0.6470 (tpt) cc_final: 0.6065 (tpt) REVERT: F 742 PHE cc_start: 0.7510 (m-80) cc_final: 0.7309 (m-10) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.6805 time to fit residues: 643.8881 Evaluate side-chains 316 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 5.9990 chunk 341 optimal weight: 0.0010 chunk 189 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 230 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 352 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 408 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 103 GLN A 443 ASN A 624 ASN B 103 GLN B 443 ASN C 91 ASN C 103 GLN C 443 ASN C 624 ASN D 91 ASN D 103 GLN D 443 ASN D 624 ASN E 103 GLN E 443 ASN F 91 ASN F 103 GLN F 443 ASN F 624 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 36294 Z= 0.152 Angle : 0.548 8.479 49086 Z= 0.267 Chirality : 0.043 0.140 5496 Planarity : 0.005 0.053 6474 Dihedral : 8.850 132.476 5094 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.62 % Allowed : 4.01 % Favored : 95.36 % 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: -1.45 (0.11), residues: 4494 helix: -0.46 (0.11), residues: 1782 sheet: 0.11 (0.20), residues: 666 loop : -1.75 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 454 HIS 0.004 0.001 HIS B 499 PHE 0.021 0.001 PHE D 674 TYR 0.018 0.001 TYR C 244 ARG 0.009 0.000 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 353 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7102 (mttp) cc_final: 0.6763 (ttpp) REVERT: A 449 MET cc_start: 0.8015 (tpt) cc_final: 0.7758 (tpt) REVERT: A 457 SER cc_start: 0.8706 (t) cc_final: 0.8392 (p) REVERT: A 720 MET cc_start: 0.4660 (mpp) cc_final: 0.4032 (mmm) REVERT: A 742 PHE cc_start: 0.7277 (m-80) cc_final: 0.6725 (m-10) REVERT: B 442 MET cc_start: 0.7418 (ppp) cc_final: 0.6970 (ttm) REVERT: B 457 SER cc_start: 0.8571 (t) cc_final: 0.8260 (p) REVERT: C 62 LYS cc_start: 0.7200 (mttp) cc_final: 0.6825 (ttpp) REVERT: C 457 SER cc_start: 0.8543 (t) cc_final: 0.8263 (p) REVERT: C 550 MET cc_start: 0.8682 (mtt) cc_final: 0.8434 (mtt) REVERT: C 611 MET cc_start: 0.7833 (tpp) cc_final: 0.7348 (ttp) REVERT: C 678 MET cc_start: 0.6471 (tpt) cc_final: 0.6190 (tpt) REVERT: C 720 MET cc_start: 0.5280 (mpp) cc_final: 0.4860 (mmm) REVERT: D 62 LYS cc_start: 0.7108 (mttp) cc_final: 0.6765 (ttpp) REVERT: D 449 MET cc_start: 0.8015 (tpt) cc_final: 0.7765 (tpt) REVERT: D 457 SER cc_start: 0.8698 (t) cc_final: 0.8383 (p) REVERT: D 720 MET cc_start: 0.4661 (mpp) cc_final: 0.4035 (mmm) REVERT: D 742 PHE cc_start: 0.7277 (m-80) cc_final: 0.6724 (m-10) REVERT: E 442 MET cc_start: 0.7424 (ppp) cc_final: 0.6969 (ttm) REVERT: E 457 SER cc_start: 0.8569 (t) cc_final: 0.8254 (p) REVERT: F 62 LYS cc_start: 0.7195 (mttp) cc_final: 0.6824 (ttpp) REVERT: F 457 SER cc_start: 0.8548 (t) cc_final: 0.8261 (p) REVERT: F 611 MET cc_start: 0.7830 (tpp) cc_final: 0.7341 (ttp) REVERT: F 678 MET cc_start: 0.6453 (tpt) cc_final: 0.6176 (tpt) REVERT: F 720 MET cc_start: 0.5283 (mpp) cc_final: 0.4863 (mmm) REVERT: F 742 PHE cc_start: 0.7642 (m-80) cc_final: 0.7362 (m-10) outliers start: 24 outliers final: 10 residues processed: 369 average time/residue: 0.5467 time to fit residues: 312.5958 Evaluate side-chains 298 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 91 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 340 optimal weight: 10.0000 chunk 278 optimal weight: 0.0000 chunk 112 optimal weight: 10.0000 chunk 409 optimal weight: 4.9990 chunk 442 optimal weight: 6.9990 chunk 364 optimal weight: 4.9990 chunk 405 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36294 Z= 0.260 Angle : 0.569 9.887 49086 Z= 0.273 Chirality : 0.045 0.142 5496 Planarity : 0.005 0.053 6474 Dihedral : 8.239 116.794 5094 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.99 % Allowed : 4.48 % Favored : 94.53 % 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: 4494 helix: 0.23 (0.12), residues: 1830 sheet: 0.16 (0.20), residues: 666 loop : -1.33 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 551 HIS 0.003 0.001 HIS B 499 PHE 0.017 0.002 PHE E 516 TYR 0.017 0.001 TYR F 244 ARG 0.009 0.001 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7135 (mttp) cc_final: 0.6801 (ttpp) REVERT: A 449 MET cc_start: 0.8027 (tpt) cc_final: 0.7358 (tpp) REVERT: A 457 SER cc_start: 0.8926 (t) cc_final: 0.8547 (p) REVERT: A 668 LYS cc_start: 0.6526 (pttt) cc_final: 0.6112 (ptpp) REVERT: A 711 ARG cc_start: 0.6979 (tmm160) cc_final: 0.6513 (tmm160) REVERT: A 742 PHE cc_start: 0.7453 (m-80) cc_final: 0.7007 (m-10) REVERT: C 62 LYS cc_start: 0.7190 (mttp) cc_final: 0.6791 (ttpp) REVERT: C 457 SER cc_start: 0.8777 (t) cc_final: 0.8387 (p) REVERT: C 611 MET cc_start: 0.7796 (tpp) cc_final: 0.7401 (ttp) REVERT: C 678 MET cc_start: 0.6544 (tpt) cc_final: 0.6300 (tpt) REVERT: C 720 MET cc_start: 0.5045 (mpp) cc_final: 0.4723 (mmm) REVERT: D 62 LYS cc_start: 0.7134 (mttp) cc_final: 0.6799 (ttpp) REVERT: D 449 MET cc_start: 0.8030 (tpt) cc_final: 0.7370 (tpp) REVERT: D 457 SER cc_start: 0.8914 (t) cc_final: 0.8542 (p) REVERT: D 668 LYS cc_start: 0.6519 (pttt) cc_final: 0.6110 (ptpp) REVERT: D 711 ARG cc_start: 0.6985 (tmm160) cc_final: 0.6515 (tmm160) REVERT: D 742 PHE cc_start: 0.7453 (m-80) cc_final: 0.7009 (m-10) REVERT: F 62 LYS cc_start: 0.7185 (mttp) cc_final: 0.6790 (ttpp) REVERT: F 457 SER cc_start: 0.8782 (t) cc_final: 0.8387 (p) REVERT: F 611 MET cc_start: 0.7789 (tpp) cc_final: 0.7392 (ttp) REVERT: F 678 MET cc_start: 0.6525 (tpt) cc_final: 0.6285 (tpt) REVERT: F 720 MET cc_start: 0.5043 (mpp) cc_final: 0.4725 (mmm) REVERT: F 742 PHE cc_start: 0.7546 (m-80) cc_final: 0.7276 (m-10) outliers start: 38 outliers final: 30 residues processed: 328 average time/residue: 0.5262 time to fit residues: 272.0144 Evaluate side-chains 304 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 760 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 434 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 389 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN A 443 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 337 GLN C 443 ASN D 91 ASN D 337 GLN D 443 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 337 GLN F 443 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36294 Z= 0.252 Angle : 0.547 9.949 49086 Z= 0.263 Chirality : 0.045 0.140 5496 Planarity : 0.004 0.052 6474 Dihedral : 7.815 109.548 5094 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 5.44 % Favored : 93.20 % 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: -0.32 (0.12), residues: 4494 helix: 0.64 (0.12), residues: 1836 sheet: 0.21 (0.21), residues: 666 loop : -1.14 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 551 HIS 0.003 0.001 HIS E 499 PHE 0.015 0.002 PHE E 516 TYR 0.016 0.001 TYR F 244 ARG 0.006 0.001 ARG E 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7153 (mttp) cc_final: 0.6807 (ttpp) REVERT: A 449 MET cc_start: 0.8003 (tpt) cc_final: 0.7347 (tpt) REVERT: A 668 LYS cc_start: 0.6519 (pttt) cc_final: 0.6084 (ptpp) REVERT: A 711 ARG cc_start: 0.6919 (tmm160) cc_final: 0.6483 (tmm160) REVERT: A 742 PHE cc_start: 0.7459 (m-80) cc_final: 0.7188 (m-10) REVERT: C 62 LYS cc_start: 0.7263 (mttp) cc_final: 0.6834 (ttpp) REVERT: C 417 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: C 457 SER cc_start: 0.8848 (t) cc_final: 0.8443 (p) REVERT: C 678 MET cc_start: 0.6538 (tpt) cc_final: 0.6283 (tpt) REVERT: C 720 MET cc_start: 0.5007 (mpp) cc_final: 0.4695 (mmm) REVERT: D 62 LYS cc_start: 0.7154 (mttp) cc_final: 0.6807 (ttpp) REVERT: D 449 MET cc_start: 0.8005 (tpt) cc_final: 0.7355 (tpt) REVERT: D 668 LYS cc_start: 0.6513 (pttt) cc_final: 0.6079 (ptpp) REVERT: D 711 ARG cc_start: 0.6918 (tmm160) cc_final: 0.6479 (tmm160) REVERT: D 742 PHE cc_start: 0.7465 (m-80) cc_final: 0.7190 (m-10) REVERT: F 62 LYS cc_start: 0.7261 (mttp) cc_final: 0.6834 (ttpp) REVERT: F 417 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: F 457 SER cc_start: 0.8853 (t) cc_final: 0.8438 (p) REVERT: F 678 MET cc_start: 0.6514 (tpt) cc_final: 0.6266 (tpt) REVERT: F 720 MET cc_start: 0.5010 (mpp) cc_final: 0.4697 (mmm) REVERT: F 742 PHE cc_start: 0.7541 (m-80) cc_final: 0.7296 (m-10) outliers start: 52 outliers final: 38 residues processed: 338 average time/residue: 0.5685 time to fit residues: 302.1117 Evaluate side-chains 310 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 270 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 760 GLN Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 0.6980 chunk 246 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 323 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 371 optimal weight: 7.9990 chunk 300 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 222 optimal weight: 0.1980 chunk 390 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 337 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 337 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 337 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36294 Z= 0.167 Angle : 0.510 8.803 49086 Z= 0.244 Chirality : 0.043 0.137 5496 Planarity : 0.004 0.050 6474 Dihedral : 7.478 105.934 5094 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.46 % Allowed : 5.96 % Favored : 92.58 % 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: -0.00 (0.13), residues: 4494 helix: 0.95 (0.13), residues: 1836 sheet: 0.28 (0.21), residues: 666 loop : -0.98 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 551 HIS 0.003 0.001 HIS B 499 PHE 0.011 0.001 PHE E 516 TYR 0.014 0.001 TYR F 244 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7156 (mttp) cc_final: 0.6808 (ttpp) REVERT: A 449 MET cc_start: 0.7961 (tpt) cc_final: 0.7350 (tpt) REVERT: A 668 LYS cc_start: 0.6518 (pttt) cc_final: 0.6075 (ptpp) REVERT: A 711 ARG cc_start: 0.6890 (tmm160) cc_final: 0.6418 (tmm160) REVERT: A 742 PHE cc_start: 0.7512 (m-80) cc_final: 0.7169 (m-10) REVERT: C 62 LYS cc_start: 0.7272 (mttp) cc_final: 0.6845 (ttpp) REVERT: C 389 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8277 (mtpt) REVERT: C 417 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: C 457 SER cc_start: 0.8840 (t) cc_final: 0.8458 (p) REVERT: C 678 MET cc_start: 0.6453 (tpt) cc_final: 0.6243 (tpt) REVERT: C 720 MET cc_start: 0.5162 (mpp) cc_final: 0.4913 (mmm) REVERT: D 62 LYS cc_start: 0.7156 (mttp) cc_final: 0.6807 (ttpp) REVERT: D 449 MET cc_start: 0.7964 (tpt) cc_final: 0.7361 (tpt) REVERT: D 668 LYS cc_start: 0.6513 (pttt) cc_final: 0.6073 (ptpp) REVERT: D 711 ARG cc_start: 0.6889 (tmm160) cc_final: 0.6413 (tmm160) REVERT: D 742 PHE cc_start: 0.7514 (m-80) cc_final: 0.7175 (m-10) REVERT: F 62 LYS cc_start: 0.7272 (mttp) cc_final: 0.6846 (ttpp) REVERT: F 389 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8278 (mtpt) REVERT: F 417 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: F 457 SER cc_start: 0.8845 (t) cc_final: 0.8456 (p) REVERT: F 678 MET cc_start: 0.6433 (tpt) cc_final: 0.6223 (tpt) REVERT: F 720 MET cc_start: 0.5163 (mpp) cc_final: 0.4914 (mmm) REVERT: F 742 PHE cc_start: 0.7524 (m-80) cc_final: 0.7286 (m-10) outliers start: 56 outliers final: 42 residues processed: 312 average time/residue: 0.5172 time to fit residues: 254.6013 Evaluate side-chains 304 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 4.9990 chunk 391 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 435 optimal weight: 1.9990 chunk 361 optimal weight: 0.1980 chunk 201 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 228 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 337 GLN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36294 Z= 0.270 Angle : 0.542 9.714 49086 Z= 0.260 Chirality : 0.045 0.143 5496 Planarity : 0.004 0.053 6474 Dihedral : 7.440 104.485 5094 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.35 % Allowed : 6.33 % Favored : 92.32 % 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: 0.00 (0.13), residues: 4494 helix: 0.93 (0.13), residues: 1872 sheet: 0.22 (0.21), residues: 666 loop : -0.94 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 551 HIS 0.003 0.001 HIS F 340 PHE 0.014 0.002 PHE E 516 TYR 0.015 0.001 TYR A 244 ARG 0.005 0.000 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7142 (mttp) cc_final: 0.6810 (ttpp) REVERT: A 69 CYS cc_start: 0.7660 (p) cc_final: 0.7408 (p) REVERT: A 449 MET cc_start: 0.7956 (tpt) cc_final: 0.7383 (tpt) REVERT: A 711 ARG cc_start: 0.6883 (tmm160) cc_final: 0.6450 (tmm160) REVERT: A 742 PHE cc_start: 0.7508 (m-80) cc_final: 0.7143 (m-10) REVERT: B 442 MET cc_start: 0.7301 (tmm) cc_final: 0.7061 (ttm) REVERT: C 62 LYS cc_start: 0.7274 (mttp) cc_final: 0.6850 (ttpp) REVERT: C 389 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8316 (mtpt) REVERT: C 417 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: C 457 SER cc_start: 0.8837 (t) cc_final: 0.8409 (p) REVERT: C 678 MET cc_start: 0.6426 (tpt) cc_final: 0.6199 (tpt) REVERT: C 720 MET cc_start: 0.4886 (mpp) cc_final: 0.4644 (mmm) REVERT: D 62 LYS cc_start: 0.7141 (mttp) cc_final: 0.6809 (ttpp) REVERT: D 69 CYS cc_start: 0.7662 (p) cc_final: 0.7408 (p) REVERT: D 449 MET cc_start: 0.7959 (tpt) cc_final: 0.7393 (tpt) REVERT: D 668 LYS cc_start: 0.6591 (pttt) cc_final: 0.6138 (ptpp) REVERT: D 711 ARG cc_start: 0.6882 (tmm160) cc_final: 0.6445 (tmm160) REVERT: D 742 PHE cc_start: 0.7513 (m-80) cc_final: 0.7147 (m-10) REVERT: E 442 MET cc_start: 0.7304 (tmm) cc_final: 0.7059 (ttm) REVERT: F 62 LYS cc_start: 0.7278 (mttp) cc_final: 0.6851 (ttpp) REVERT: F 389 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8318 (mtpt) REVERT: F 417 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: F 457 SER cc_start: 0.8845 (t) cc_final: 0.8408 (p) REVERT: F 678 MET cc_start: 0.6404 (tpt) cc_final: 0.6186 (tpt) REVERT: F 720 MET cc_start: 0.4883 (mpp) cc_final: 0.4646 (mmm) REVERT: F 742 PHE cc_start: 0.7513 (m-80) cc_final: 0.7226 (m-10) outliers start: 52 outliers final: 34 residues processed: 309 average time/residue: 0.5391 time to fit residues: 267.1008 Evaluate side-chains 297 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 243 optimal weight: 0.0000 chunk 433 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN A 443 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN D 91 ASN D 337 GLN D 443 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36294 Z= 0.179 Angle : 0.514 9.680 49086 Z= 0.243 Chirality : 0.044 0.137 5496 Planarity : 0.004 0.052 6474 Dihedral : 7.092 99.566 5094 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.41 % Allowed : 6.48 % Favored : 92.11 % 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: 0.29 (0.13), residues: 4494 helix: 1.15 (0.13), residues: 1866 sheet: 0.31 (0.21), residues: 666 loop : -0.75 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.003 0.001 HIS E 499 PHE 0.015 0.001 PHE F 363 TYR 0.014 0.001 TYR A 244 ARG 0.006 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7129 (mttp) cc_final: 0.6798 (ttpp) REVERT: A 152 PHE cc_start: 0.6192 (p90) cc_final: 0.5702 (p90) REVERT: A 449 MET cc_start: 0.7925 (tpt) cc_final: 0.7373 (tpt) REVERT: A 711 ARG cc_start: 0.7026 (tmm160) cc_final: 0.6582 (tmm160) REVERT: B 229 LEU cc_start: 0.7691 (tt) cc_final: 0.7137 (mt) REVERT: C 62 LYS cc_start: 0.7275 (mttp) cc_final: 0.6859 (ttpp) REVERT: C 417 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: C 457 SER cc_start: 0.8759 (t) cc_final: 0.8375 (p) REVERT: C 720 MET cc_start: 0.4872 (mpp) cc_final: 0.4637 (mmm) REVERT: D 62 LYS cc_start: 0.7128 (mttp) cc_final: 0.6796 (ttpp) REVERT: D 152 PHE cc_start: 0.6219 (p90) cc_final: 0.5729 (p90) REVERT: D 449 MET cc_start: 0.7926 (tpt) cc_final: 0.7381 (tpt) REVERT: D 711 ARG cc_start: 0.7025 (tmm160) cc_final: 0.6580 (tmm160) REVERT: E 229 LEU cc_start: 0.7690 (tt) cc_final: 0.7133 (mt) REVERT: F 62 LYS cc_start: 0.7276 (mttp) cc_final: 0.6860 (ttpp) REVERT: F 417 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: F 457 SER cc_start: 0.8766 (t) cc_final: 0.8375 (p) REVERT: F 720 MET cc_start: 0.4874 (mpp) cc_final: 0.4640 (mmm) REVERT: F 742 PHE cc_start: 0.7555 (m-80) cc_final: 0.7265 (m-10) outliers start: 54 outliers final: 40 residues processed: 303 average time/residue: 0.5162 time to fit residues: 246.4574 Evaluate side-chains 290 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN A 401 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 337 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 337 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 337 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 36294 Z= 0.371 Angle : 0.603 10.745 49086 Z= 0.289 Chirality : 0.047 0.150 5496 Planarity : 0.005 0.056 6474 Dihedral : 7.402 100.328 5094 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.46 % Allowed : 6.80 % Favored : 91.74 % 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: 0.10 (0.13), residues: 4494 helix: 0.95 (0.12), residues: 1866 sheet: 0.41 (0.22), residues: 618 loop : -0.84 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 551 HIS 0.004 0.001 HIS E 384 PHE 0.018 0.002 PHE A 682 TYR 0.015 0.002 TYR A 244 ARG 0.008 0.001 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 254 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7136 (mttp) cc_final: 0.6841 (ttpp) REVERT: A 69 CYS cc_start: 0.7613 (p) cc_final: 0.7383 (p) REVERT: A 152 PHE cc_start: 0.6198 (p90) cc_final: 0.5721 (p90) REVERT: A 449 MET cc_start: 0.7934 (tpt) cc_final: 0.7332 (tpt) REVERT: A 711 ARG cc_start: 0.6972 (tmm160) cc_final: 0.6539 (tmm160) REVERT: C 62 LYS cc_start: 0.7268 (mttp) cc_final: 0.6855 (ttpp) REVERT: C 417 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 457 SER cc_start: 0.8786 (t) cc_final: 0.8385 (p) REVERT: C 720 MET cc_start: 0.4557 (mpp) cc_final: 0.4333 (mmm) REVERT: D 62 LYS cc_start: 0.7137 (mttp) cc_final: 0.6839 (ttpp) REVERT: D 69 CYS cc_start: 0.7611 (p) cc_final: 0.7381 (p) REVERT: D 152 PHE cc_start: 0.6227 (p90) cc_final: 0.5747 (p90) REVERT: D 449 MET cc_start: 0.7937 (tpt) cc_final: 0.7347 (tpt) REVERT: D 711 ARG cc_start: 0.6967 (tmm160) cc_final: 0.6531 (tmm160) REVERT: F 62 LYS cc_start: 0.7273 (mttp) cc_final: 0.6857 (ttpp) REVERT: F 417 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: F 457 SER cc_start: 0.8795 (t) cc_final: 0.8386 (p) REVERT: F 720 MET cc_start: 0.4556 (mpp) cc_final: 0.4332 (mmm) REVERT: F 742 PHE cc_start: 0.7621 (m-80) cc_final: 0.7320 (m-10) outliers start: 56 outliers final: 50 residues processed: 298 average time/residue: 0.4984 time to fit residues: 237.7630 Evaluate side-chains 299 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 247 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 760 GLN Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 404 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 317 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 chunk 382 optimal weight: 5.9990 chunk 402 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36294 Z= 0.223 Angle : 0.554 9.278 49086 Z= 0.264 Chirality : 0.044 0.142 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.228 98.387 5094 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.25 % Allowed : 7.27 % Favored : 91.48 % 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: 0.26 (0.13), residues: 4494 helix: 1.10 (0.13), residues: 1866 sheet: 0.48 (0.22), residues: 618 loop : -0.77 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 454 HIS 0.003 0.001 HIS E 499 PHE 0.015 0.001 PHE F 363 TYR 0.020 0.001 TYR B 244 ARG 0.005 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7098 (mttp) cc_final: 0.6796 (ttpp) REVERT: A 69 CYS cc_start: 0.7607 (p) cc_final: 0.7381 (p) REVERT: A 152 PHE cc_start: 0.6204 (p90) cc_final: 0.5724 (p90) REVERT: A 449 MET cc_start: 0.7954 (tpt) cc_final: 0.7408 (tpt) REVERT: A 711 ARG cc_start: 0.7064 (tmm160) cc_final: 0.6667 (tmm160) REVERT: C 62 LYS cc_start: 0.7265 (mttp) cc_final: 0.6856 (ttpp) REVERT: C 222 LEU cc_start: 0.8779 (tp) cc_final: 0.8355 (mm) REVERT: C 417 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: C 457 SER cc_start: 0.8756 (t) cc_final: 0.8361 (p) REVERT: C 720 MET cc_start: 0.4388 (mpp) cc_final: 0.4144 (mmm) REVERT: C 741 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7654 (mtp85) REVERT: D 62 LYS cc_start: 0.7099 (mttp) cc_final: 0.6795 (ttpp) REVERT: D 69 CYS cc_start: 0.7602 (p) cc_final: 0.7372 (p) REVERT: D 152 PHE cc_start: 0.6232 (p90) cc_final: 0.5750 (p90) REVERT: D 449 MET cc_start: 0.7962 (tpt) cc_final: 0.7420 (tpt) REVERT: D 711 ARG cc_start: 0.7064 (tmm160) cc_final: 0.6661 (tmm160) REVERT: F 62 LYS cc_start: 0.7269 (mttp) cc_final: 0.6854 (ttpp) REVERT: F 417 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: F 457 SER cc_start: 0.8768 (t) cc_final: 0.8363 (p) REVERT: F 720 MET cc_start: 0.4387 (mpp) cc_final: 0.4144 (mmm) REVERT: F 742 PHE cc_start: 0.7595 (m-80) cc_final: 0.7292 (m-10) outliers start: 48 outliers final: 40 residues processed: 288 average time/residue: 0.5075 time to fit residues: 235.1941 Evaluate side-chains 287 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 448 optimal weight: 0.9980 chunk 412 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 chunk 218 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36294 Z= 0.195 Angle : 0.537 9.474 49086 Z= 0.255 Chirality : 0.044 0.139 5496 Planarity : 0.004 0.053 6474 Dihedral : 7.076 95.035 5094 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.15 % Allowed : 7.37 % Favored : 91.48 % 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: 0.40 (0.13), residues: 4494 helix: 1.21 (0.13), residues: 1866 sheet: 0.51 (0.22), residues: 624 loop : -0.69 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 454 HIS 0.003 0.001 HIS E 499 PHE 0.014 0.001 PHE F 363 TYR 0.018 0.001 TYR B 244 ARG 0.003 0.000 ARG E 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 4.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7102 (mttp) cc_final: 0.6803 (ttpp) REVERT: A 69 CYS cc_start: 0.7623 (p) cc_final: 0.7394 (p) REVERT: A 152 PHE cc_start: 0.6207 (p90) cc_final: 0.5719 (p90) REVERT: A 449 MET cc_start: 0.7960 (tpt) cc_final: 0.7423 (tpt) REVERT: A 711 ARG cc_start: 0.7069 (tmm160) cc_final: 0.6655 (tmm160) REVERT: C 62 LYS cc_start: 0.7286 (mttp) cc_final: 0.6863 (ttpp) REVERT: C 417 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 457 SER cc_start: 0.8776 (t) cc_final: 0.8350 (p) REVERT: C 720 MET cc_start: 0.4374 (mpp) cc_final: 0.4134 (mmm) REVERT: D 62 LYS cc_start: 0.7099 (mttp) cc_final: 0.6800 (ttpp) REVERT: D 69 CYS cc_start: 0.7615 (p) cc_final: 0.7384 (p) REVERT: D 152 PHE cc_start: 0.6236 (p90) cc_final: 0.5744 (p90) REVERT: D 449 MET cc_start: 0.7964 (tpt) cc_final: 0.7435 (tpt) REVERT: D 711 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6650 (tmm160) REVERT: F 62 LYS cc_start: 0.7280 (mttp) cc_final: 0.6865 (ttpp) REVERT: F 417 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: F 457 SER cc_start: 0.8785 (t) cc_final: 0.8351 (p) REVERT: F 720 MET cc_start: 0.4371 (mpp) cc_final: 0.4131 (mmm) REVERT: F 742 PHE cc_start: 0.7587 (m-80) cc_final: 0.7288 (m-10) outliers start: 44 outliers final: 40 residues processed: 277 average time/residue: 0.4875 time to fit residues: 217.5294 Evaluate side-chains 283 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 0.9990 chunk 380 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 99 optimal weight: 0.0570 chunk 357 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 367 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN D 337 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.177249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113642 restraints weight = 47200.839| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.85 r_work: 0.3157 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36294 Z= 0.194 Angle : 0.528 9.376 49086 Z= 0.249 Chirality : 0.044 0.137 5496 Planarity : 0.004 0.053 6474 Dihedral : 6.881 87.582 5094 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.25 % Allowed : 7.47 % Favored : 91.28 % 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: 0.54 (0.13), residues: 4494 helix: 1.29 (0.13), residues: 1872 sheet: 0.63 (0.22), residues: 618 loop : -0.58 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 454 HIS 0.003 0.001 HIS B 499 PHE 0.013 0.001 PHE C 363 TYR 0.017 0.001 TYR E 244 ARG 0.004 0.000 ARG F 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7284.48 seconds wall clock time: 131 minutes 27.07 seconds (7887.07 seconds total)