Starting phenix.real_space_refine on Tue Mar 19 21:08:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/03_2024/7nku_12448_updated.pdb" } resolution = 3.4 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= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 B 6 2.79 5 C 15834 2.51 5 N 4344 2.21 5 O 4992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 708": "OD1" <-> "OD2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ASP 433": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 708": "OD1" <-> "OD2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F ASP 421": "OD1" <-> "OD2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F ASP 517": "OD1" <-> "OD2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F GLU 738": "OE1" <-> "OE2" Residue "F ASP 741": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25332 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "C" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "E" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "F" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.53, per 1000 atoms: 0.53 Number of scatterers: 25332 At special positions: 0 Unit cell: (138.86, 136.74, 98.58, 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 120 16.00 P 36 15.00 O 4992 8.00 N 4344 7.00 C 15834 6.00 B 6 5.00 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.65 Conformation dependent library (CDL) restraints added in 4.5 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 12 sheets defined 48.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.854A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 416 through 429 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 454 through 475 removed outlier: 4.017A pdb=" N THR A 475 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 removed outlier: 4.174A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 537 Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 584 through 587 No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 593 through 607 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 627 through 644 removed outlier: 5.147A pdb=" N ALA A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASN A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 721 through 738 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.632A pdb=" N ARG A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 266 Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.779A pdb=" N ALA B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 454 through 475 removed outlier: 4.205A pdb=" N THR B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 4.420A pdb=" N ASP B 497 " --> pdb=" O SER B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 537 Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 584 through 587 No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 591 through 607 removed outlier: 3.554A pdb=" N GLU B 595 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 627 through 644 removed outlier: 5.421A pdb=" N ALA B 633 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'B' and resid 721 through 738 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 320 through 336 removed outlier: 4.125A pdb=" N ALA C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'C' and resid 454 through 475 removed outlier: 4.067A pdb=" N THR C 475 " --> pdb=" O GLY C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 498 removed outlier: 4.218A pdb=" N ASP C 497 " --> pdb=" O SER C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 537 Proline residue: C 535 - end of helix Processing helix chain 'C' and resid 539 through 545 Processing helix chain 'C' and resid 564 through 572 Processing helix chain 'C' and resid 583 through 585 No H-bonds generated for 'chain 'C' and resid 583 through 585' Processing helix chain 'C' and resid 591 through 607 removed outlier: 4.022A pdb=" N GLU C 595 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 627 through 644 removed outlier: 5.505A pdb=" N ALA C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN C 634 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 721 through 738 Processing helix chain 'C' and resid 747 through 756 Processing helix chain 'C' and resid 763 through 774 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 292 through 302 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 320 through 336 removed outlier: 4.064A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 363 through 374 Processing helix chain 'D' and resid 397 through 400 No H-bonds generated for 'chain 'D' and resid 397 through 400' Processing helix chain 'D' and resid 416 through 429 Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'D' and resid 454 through 475 removed outlier: 4.510A pdb=" N THR D 475 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 removed outlier: 4.300A pdb=" N ASP D 497 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 537 Proline residue: D 535 - end of helix Processing helix chain 'D' and resid 539 through 545 Processing helix chain 'D' and resid 564 through 572 Processing helix chain 'D' and resid 583 through 586 No H-bonds generated for 'chain 'D' and resid 583 through 586' Processing helix chain 'D' and resid 591 through 607 removed outlier: 4.450A pdb=" N ALA D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'D' and resid 629 through 645 removed outlier: 5.246A pdb=" N ASN D 634 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N HIS D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 709 through 715 Processing helix chain 'D' and resid 721 through 738 Processing helix chain 'D' and resid 747 through 756 Processing helix chain 'D' and resid 763 through 774 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 292 through 302 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 320 through 336 removed outlier: 3.939A pdb=" N ALA E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 363 through 374 Processing helix chain 'E' and resid 397 through 400 No H-bonds generated for 'chain 'E' and resid 397 through 400' Processing helix chain 'E' and resid 416 through 429 Processing helix chain 'E' and resid 439 through 447 Processing helix chain 'E' and resid 454 through 475 removed outlier: 4.352A pdb=" N THR E 475 " --> pdb=" O GLY E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 498 removed outlier: 4.131A pdb=" N ASP E 497 " --> pdb=" O SER E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 537 Proline residue: E 535 - end of helix Processing helix chain 'E' and resid 539 through 545 Processing helix chain 'E' and resid 564 through 574 Processing helix chain 'E' and resid 583 through 586 No H-bonds generated for 'chain 'E' and resid 583 through 586' Processing helix chain 'E' and resid 591 through 607 Processing helix chain 'E' and resid 618 through 620 No H-bonds generated for 'chain 'E' and resid 618 through 620' Processing helix chain 'E' and resid 627 through 645 removed outlier: 3.685A pdb=" N SER E 631 " --> pdb=" O SER E 628 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 633 " --> pdb=" O THR E 630 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASN E 634 " --> pdb=" O SER E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 667 through 669 No H-bonds generated for 'chain 'E' and resid 667 through 669' Processing helix chain 'E' and resid 686 through 696 Processing helix chain 'E' and resid 709 through 715 Processing helix chain 'E' and resid 721 through 738 Processing helix chain 'E' and resid 747 through 755 Processing helix chain 'E' and resid 763 through 775 Processing helix chain 'F' and resid 251 through 263 Processing helix chain 'F' and resid 269 through 272 No H-bonds generated for 'chain 'F' and resid 269 through 272' Processing helix chain 'F' and resid 292 through 302 Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 320 through 336 removed outlier: 4.116A pdb=" N ALA F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 363 through 374 Processing helix chain 'F' and resid 397 through 400 No H-bonds generated for 'chain 'F' and resid 397 through 400' Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'F' and resid 439 through 447 Processing helix chain 'F' and resid 454 through 475 removed outlier: 4.381A pdb=" N THR F 475 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 498 Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 539 through 545 Processing helix chain 'F' and resid 564 through 574 Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 591 through 607 Processing helix chain 'F' and resid 618 through 620 No H-bonds generated for 'chain 'F' and resid 618 through 620' Processing helix chain 'F' and resid 627 through 645 removed outlier: 5.121A pdb=" N ASN F 634 " --> pdb=" O THR F 630 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS F 635 " --> pdb=" O SER F 631 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 636 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 686 through 696 Processing helix chain 'F' and resid 703 through 705 No H-bonds generated for 'chain 'F' and resid 703 through 705' Processing helix chain 'F' and resid 709 through 715 Processing helix chain 'F' and resid 721 through 738 Processing helix chain 'F' and resid 747 through 756 Processing helix chain 'F' and resid 763 through 775 Processing sheet with id= A, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.640A pdb=" N SER A 340 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 386 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 342 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 388 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 344 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 306 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE A 343 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 308 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP A 345 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 310 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 677 through 680 removed outlier: 8.594A pdb=" N VAL A 553 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 655 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 555 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 657 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 611 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A 656 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A 613 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 658 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 615 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 577 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 614 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 579 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP A 616 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 581 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.588A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE B 310 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 580 through 582 removed outlier: 7.535A pdb=" N VAL B 581 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 614 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 554 " --> pdb=" O ASP B 676 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS B 678 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR B 556 " --> pdb=" O HIS B 678 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 680 " --> pdb=" O TYR B 556 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 306 through 310 removed outlier: 4.487A pdb=" N ASP C 345 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU C 283 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU C 408 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 577 through 582 removed outlier: 6.176A pdb=" N LEU C 554 " --> pdb=" O ASP C 676 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS C 678 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C 556 " --> pdb=" O HIS C 678 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 680 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.445A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE D 310 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 677 through 680 removed outlier: 8.602A pdb=" N VAL D 553 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE D 655 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 555 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 657 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER D 611 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 656 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN D 577 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE D 614 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 579 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP D 616 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 581 " --> pdb=" O ASP D 616 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 407 through 409 removed outlier: 6.518A pdb=" N SER E 340 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE E 386 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE E 342 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA E 388 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 344 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS E 306 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 343 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 308 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP E 345 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE E 310 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 677 through 680 removed outlier: 8.805A pdb=" N VAL E 553 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE E 655 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU E 555 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 657 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER E 611 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL E 656 " --> pdb=" O SER E 611 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 613 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA E 658 " --> pdb=" O ILE E 613 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE E 615 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP E 616 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 407 through 410 removed outlier: 6.412A pdb=" N SER F 340 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE F 386 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP F 345 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 310 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 677 through 680 removed outlier: 8.762A pdb=" N VAL F 553 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 655 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU F 555 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA F 657 " --> pdb=" O LEU F 555 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER F 611 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL F 656 " --> pdb=" O SER F 611 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN F 577 " --> pdb=" O ILE F 612 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 614 " --> pdb=" O ASN F 577 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU F 579 " --> pdb=" O PHE F 614 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP F 616 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 581 " --> pdb=" O ASP F 616 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2538 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: 8.24 Time building geometry restraints manager: 11.33 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: 8727 1.37 - 1.51: 7864 1.51 - 1.66: 8987 1.66 - 1.80: 163 1.80 - 1.95: 41 Bond restraints: 25782 Sorted by residual: bond pdb=" C14 TDB A 903 " pdb=" S1 TDB A 903 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C14 TDB F 801 " pdb=" S1 TDB F 801 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C14 TDB D 801 " pdb=" S1 TDB D 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C14 TDB C 801 " pdb=" S1 TDB C 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C14 TDB D 804 " pdb=" S1 TDB D 804 " ideal model delta sigma weight residual 1.717 1.866 -0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 25777 not shown) Histogram of bond angle deviations from ideal: 88.75 - 97.84: 7 97.84 - 106.93: 974 106.93 - 116.02: 16327 116.02 - 125.11: 17317 125.11 - 134.20: 361 Bond angle restraints: 34986 Sorted by residual: angle pdb=" C13 TDB D 804 " pdb=" B1 TDB D 804 " pdb=" O1 TDB D 804 " ideal model delta sigma weight residual 127.55 104.96 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C13 TDB A 904 " pdb=" B1 TDB A 904 " pdb=" O1 TDB A 904 " ideal model delta sigma weight residual 127.55 105.30 22.25 3.00e+00 1.11e-01 5.50e+01 angle pdb=" O15 TDB D 801 " pdb=" S15 TDB D 801 " pdb=" O16 TDB D 801 " ideal model delta sigma weight residual 118.86 102.15 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C13 TDB F 801 " pdb=" B1 TDB F 801 " pdb=" O1 TDB F 801 " ideal model delta sigma weight residual 127.55 110.88 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O15 TDB C 801 " pdb=" S15 TDB C 801 " pdb=" O16 TDB C 801 " ideal model delta sigma weight residual 118.86 102.27 16.59 3.00e+00 1.11e-01 3.06e+01 ... (remaining 34981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 15472 33.37 - 66.74: 384 66.74 - 100.11: 27 100.11 - 133.48: 1 133.48 - 166.85: 10 Dihedral angle restraints: 15894 sinusoidal: 6552 harmonic: 9342 Sorted by residual: dihedral pdb=" CA ASN A 588 " pdb=" C ASN A 588 " pdb=" N LYS A 589 " pdb=" CA LYS A 589 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLU D 573 " pdb=" C GLU D 573 " pdb=" N SER D 574 " pdb=" CA SER D 574 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU A 573 " pdb=" C GLU A 573 " pdb=" N SER A 574 " pdb=" CA SER A 574 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 15891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3094 0.058 - 0.115: 803 0.115 - 0.173: 114 0.173 - 0.231: 5 0.231 - 0.288: 4 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CB ILE A 498 " pdb=" CA ILE A 498 " pdb=" CG1 ILE A 498 " pdb=" CG2 ILE A 498 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 457 " pdb=" CB LEU B 457 " pdb=" CD1 LEU B 457 " pdb=" CD2 LEU B 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 457 " pdb=" CB LEU F 457 " pdb=" CD1 LEU F 457 " pdb=" CD2 LEU F 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4017 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 804 " -0.269 2.00e-02 2.50e+03 2.93e-01 2.57e+03 pdb=" C12 TDB D 804 " -0.195 2.00e-02 2.50e+03 pdb=" C13 TDB D 804 " -0.145 2.00e-02 2.50e+03 pdb=" C14 TDB D 804 " 0.061 2.00e-02 2.50e+03 pdb=" C2 TDB D 804 " 0.150 2.00e-02 2.50e+03 pdb=" C7 TDB D 804 " -0.063 2.00e-02 2.50e+03 pdb=" C8 TDB D 804 " -0.106 2.00e-02 2.50e+03 pdb=" N1 TDB D 804 " -0.190 2.00e-02 2.50e+03 pdb=" N2 TDB D 804 " 0.033 2.00e-02 2.50e+03 pdb=" O1 TDB D 804 " 0.841 2.00e-02 2.50e+03 pdb=" S1 TDB D 804 " 0.169 2.00e-02 2.50e+03 pdb=" S15 TDB D 804 " -0.286 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB A 904 " 0.265 2.00e-02 2.50e+03 2.92e-01 2.55e+03 pdb=" C12 TDB A 904 " 0.191 2.00e-02 2.50e+03 pdb=" C13 TDB A 904 " 0.140 2.00e-02 2.50e+03 pdb=" C14 TDB A 904 " -0.061 2.00e-02 2.50e+03 pdb=" C2 TDB A 904 " -0.147 2.00e-02 2.50e+03 pdb=" C7 TDB A 904 " 0.066 2.00e-02 2.50e+03 pdb=" C8 TDB A 904 " 0.107 2.00e-02 2.50e+03 pdb=" N1 TDB A 904 " 0.189 2.00e-02 2.50e+03 pdb=" N2 TDB A 904 " -0.032 2.00e-02 2.50e+03 pdb=" O1 TDB A 904 " -0.839 2.00e-02 2.50e+03 pdb=" S1 TDB A 904 " -0.168 2.00e-02 2.50e+03 pdb=" S15 TDB A 904 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 801 " -0.246 2.00e-02 2.50e+03 2.48e-01 1.84e+03 pdb=" C12 TDB D 801 " -0.173 2.00e-02 2.50e+03 pdb=" C13 TDB D 801 " -0.120 2.00e-02 2.50e+03 pdb=" C14 TDB D 801 " 0.058 2.00e-02 2.50e+03 pdb=" C2 TDB D 801 " 0.144 2.00e-02 2.50e+03 pdb=" C7 TDB D 801 " -0.057 2.00e-02 2.50e+03 pdb=" C8 TDB D 801 " -0.096 2.00e-02 2.50e+03 pdb=" N1 TDB D 801 " -0.147 2.00e-02 2.50e+03 pdb=" N2 TDB D 801 " 0.039 2.00e-02 2.50e+03 pdb=" O1 TDB D 801 " 0.694 2.00e-02 2.50e+03 pdb=" S1 TDB D 801 " 0.158 2.00e-02 2.50e+03 pdb=" S15 TDB D 801 " -0.255 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 324 2.57 - 3.15: 23516 3.15 - 3.73: 40853 3.73 - 4.32: 54964 4.32 - 4.90: 86253 Nonbonded interactions: 205910 Sorted by model distance: nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 1.986 2.440 nonbonded pdb=" OG SER D 720 " pdb=" OE1 GLU D 723 " model vdw 1.992 2.440 nonbonded pdb=" O2B AGS E 901 " pdb=" O2G AGS E 901 " model vdw 1.998 2.440 nonbonded pdb=" O2B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.007 2.440 nonbonded pdb=" O2B AGS D 802 " pdb=" O2G AGS D 802 " model vdw 2.020 2.440 ... (remaining 205905 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' and (resid 239 through 780 or resid 902)) selection = (chain 'B' and (resid 239 through 780 or resid 902)) selection = (chain 'C' and (resid 239 through 780 or resid 802)) selection = (chain 'D' and (resid 239 through 780 or resid 802)) selection = (chain 'E' and (resid 239 through 780 or resid 902)) selection = (chain 'F' and (resid 239 through 780 or resid 802)) } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.000 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 69.170 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 25782 Z= 0.488 Angle : 0.941 22.586 34986 Z= 0.469 Chirality : 0.052 0.288 4020 Planarity : 0.011 0.293 4488 Dihedral : 15.331 166.853 9870 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.63 (0.15), residues: 3240 helix: 0.00 (0.13), residues: 1548 sheet: -0.10 (0.28), residues: 402 loop : -0.90 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 515 HIS 0.011 0.001 HIS B 306 PHE 0.024 0.002 PHE D 700 TYR 0.053 0.002 TYR C 444 ARG 0.018 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1040 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 VAL cc_start: 0.8921 (t) cc_final: 0.8663 (p) REVERT: A 333 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 335 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7803 (mtp-110) REVERT: A 408 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6676 (mt-10) REVERT: A 443 LYS cc_start: 0.8806 (mmpt) cc_final: 0.8277 (mmmm) REVERT: A 444 TYR cc_start: 0.8545 (t80) cc_final: 0.7964 (t80) REVERT: A 448 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7853 (mttt) REVERT: A 452 TYR cc_start: 0.7994 (m-80) cc_final: 0.7519 (m-80) REVERT: A 488 LEU cc_start: 0.8349 (tt) cc_final: 0.7965 (tp) REVERT: A 489 LYS cc_start: 0.8420 (mppt) cc_final: 0.8033 (mppt) REVERT: A 492 GLU cc_start: 0.7734 (mp0) cc_final: 0.7340 (mp0) REVERT: A 499 ARG cc_start: 0.6922 (tpm170) cc_final: 0.4573 (tpp-160) REVERT: A 513 VAL cc_start: 0.8820 (m) cc_final: 0.8345 (p) REVERT: A 514 TYR cc_start: 0.8541 (m-10) cc_final: 0.8114 (m-10) REVERT: A 523 GLU cc_start: 0.7370 (tp30) cc_final: 0.6920 (tp30) REVERT: A 540 GLU cc_start: 0.7316 (pp20) cc_final: 0.7067 (pp20) REVERT: A 548 SER cc_start: 0.8817 (m) cc_final: 0.8177 (p) REVERT: A 556 TYR cc_start: 0.8317 (p90) cc_final: 0.7963 (p90) REVERT: A 572 THR cc_start: 0.8409 (m) cc_final: 0.8196 (p) REVERT: A 582 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8065 (mmmm) REVERT: A 595 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7796 (mp0) REVERT: A 661 ARG cc_start: 0.7187 (mmm160) cc_final: 0.6823 (mmm160) REVERT: A 663 ASP cc_start: 0.7576 (p0) cc_final: 0.7108 (p0) REVERT: A 664 GLU cc_start: 0.7850 (pt0) cc_final: 0.7506 (pt0) REVERT: A 691 GLU cc_start: 0.8195 (tp30) cc_final: 0.7547 (tp30) REVERT: A 694 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8688 (mttp) REVERT: A 695 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8312 (tptp) REVERT: A 698 LYS cc_start: 0.8980 (ptmm) cc_final: 0.8533 (ptpp) REVERT: A 717 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 730 GLU cc_start: 0.7769 (tp30) cc_final: 0.7562 (tp30) REVERT: A 751 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 752 LYS cc_start: 0.8725 (tttm) cc_final: 0.8357 (ttmm) REVERT: A 755 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8454 (ttmt) REVERT: A 770 GLU cc_start: 0.7384 (mp0) cc_final: 0.7129 (mp0) REVERT: B 252 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8025 (ttmm) REVERT: B 262 GLU cc_start: 0.7790 (tp30) cc_final: 0.7459 (tp30) REVERT: B 266 HIS cc_start: 0.8176 (m-70) cc_final: 0.7662 (m170) REVERT: B 308 LEU cc_start: 0.8644 (mp) cc_final: 0.8068 (mp) REVERT: B 328 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7919 (ttm110) REVERT: B 333 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6611 (tm-30) REVERT: B 335 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7727 (mtp-110) REVERT: B 373 LEU cc_start: 0.8146 (tt) cc_final: 0.7911 (tt) REVERT: B 377 MET cc_start: 0.6840 (mpp) cc_final: 0.6558 (mpp) REVERT: B 421 ASP cc_start: 0.8219 (t0) cc_final: 0.7974 (t0) REVERT: B 444 TYR cc_start: 0.8494 (t80) cc_final: 0.8158 (t80) REVERT: B 463 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 485 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8138 (mmtp) REVERT: B 488 LEU cc_start: 0.8494 (tp) cc_final: 0.8079 (tt) REVERT: B 492 GLU cc_start: 0.7751 (mp0) cc_final: 0.7511 (mp0) REVERT: B 493 SER cc_start: 0.8825 (t) cc_final: 0.8601 (p) REVERT: B 497 ASP cc_start: 0.7478 (t0) cc_final: 0.7053 (t0) REVERT: B 514 TYR cc_start: 0.8794 (m-10) cc_final: 0.8542 (m-80) REVERT: B 530 GLU cc_start: 0.7904 (tt0) cc_final: 0.7143 (tt0) REVERT: B 540 GLU cc_start: 0.7540 (pp20) cc_final: 0.7332 (pp20) REVERT: B 572 THR cc_start: 0.8371 (m) cc_final: 0.8137 (m) REVERT: B 600 GLU cc_start: 0.7756 (pp20) cc_final: 0.7233 (pp20) REVERT: B 638 THR cc_start: 0.8589 (t) cc_final: 0.8206 (p) REVERT: B 642 ASN cc_start: 0.8319 (t0) cc_final: 0.8052 (t0) REVERT: B 643 GLU cc_start: 0.7902 (tp30) cc_final: 0.7614 (tp30) REVERT: B 661 ARG cc_start: 0.7448 (tpt170) cc_final: 0.6726 (tpt170) REVERT: B 664 GLU cc_start: 0.7892 (pt0) cc_final: 0.7584 (pt0) REVERT: B 680 TYR cc_start: 0.8686 (t80) cc_final: 0.8364 (t80) REVERT: B 694 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8696 (mtpp) REVERT: B 695 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8356 (tptp) REVERT: B 696 CYS cc_start: 0.8061 (t) cc_final: 0.7800 (t) REVERT: B 715 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7555 (ttp80) REVERT: B 717 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 751 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6904 (tm-30) REVERT: B 752 LYS cc_start: 0.8684 (tttm) cc_final: 0.8317 (ttmm) REVERT: B 755 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8414 (ttmm) REVERT: C 255 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 262 GLU cc_start: 0.7859 (tp30) cc_final: 0.7619 (tp30) REVERT: C 292 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8640 (mttp) REVERT: C 308 LEU cc_start: 0.8780 (mp) cc_final: 0.8304 (mp) REVERT: C 333 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 346 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7058 (mm-30) REVERT: C 382 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6884 (mtmm) REVERT: C 391 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6995 (ptt90) REVERT: C 393 ASN cc_start: 0.8410 (m-40) cc_final: 0.8150 (m-40) REVERT: C 426 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8106 (mm-40) REVERT: C 443 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8489 (mmtp) REVERT: C 453 VAL cc_start: 0.9075 (p) cc_final: 0.8745 (m) REVERT: C 467 LYS cc_start: 0.8422 (mttm) cc_final: 0.8214 (mmtp) REVERT: C 468 THR cc_start: 0.8560 (m) cc_final: 0.8032 (p) REVERT: C 493 SER cc_start: 0.8845 (t) cc_final: 0.8314 (p) REVERT: C 497 ASP cc_start: 0.7448 (t0) cc_final: 0.7195 (t0) REVERT: C 512 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7970 (mmmt) REVERT: C 522 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7375 (mm-30) REVERT: C 525 LYS cc_start: 0.8305 (tppp) cc_final: 0.8030 (tppp) REVERT: C 540 GLU cc_start: 0.7551 (pp20) cc_final: 0.7283 (pp20) REVERT: C 582 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8322 (mmmm) REVERT: C 595 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 599 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7721 (mtt-85) REVERT: C 661 ARG cc_start: 0.7405 (tpt170) cc_final: 0.6493 (tpt90) REVERT: C 671 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7887 (ttm-80) REVERT: C 691 GLU cc_start: 0.8165 (tp30) cc_final: 0.7737 (tp30) REVERT: C 751 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 755 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8410 (tmtt) REVERT: C 770 GLU cc_start: 0.7471 (tp30) cc_final: 0.6970 (tp30) REVERT: C 774 LEU cc_start: 0.8945 (mm) cc_final: 0.8728 (mm) REVERT: D 247 VAL cc_start: 0.8774 (t) cc_final: 0.8540 (p) REVERT: D 252 LYS cc_start: 0.8264 (tppp) cc_final: 0.8053 (tppp) REVERT: D 254 ILE cc_start: 0.8886 (mm) cc_final: 0.8605 (mt) REVERT: D 292 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8409 (mttp) REVERT: D 297 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6411 (mmm160) REVERT: D 301 ASN cc_start: 0.7438 (m110) cc_final: 0.7160 (m110) REVERT: D 308 LEU cc_start: 0.8548 (mp) cc_final: 0.8285 (mp) REVERT: D 328 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8044 (ttm110) REVERT: D 333 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6432 (tm-30) REVERT: D 426 GLN cc_start: 0.8417 (tp40) cc_final: 0.7913 (tp40) REVERT: D 443 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8457 (mmtp) REVERT: D 444 TYR cc_start: 0.8431 (t80) cc_final: 0.8118 (t80) REVERT: D 463 GLU cc_start: 0.8331 (tp30) cc_final: 0.8087 (tp30) REVERT: D 489 LYS cc_start: 0.8515 (mppt) cc_final: 0.8221 (mppt) REVERT: D 497 ASP cc_start: 0.7776 (t0) cc_final: 0.7564 (t0) REVERT: D 512 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7902 (ttmm) REVERT: D 517 ASP cc_start: 0.8547 (m-30) cc_final: 0.8339 (m-30) REVERT: D 523 GLU cc_start: 0.7478 (tp30) cc_final: 0.6843 (tp30) REVERT: D 542 PHE cc_start: 0.8845 (m-80) cc_final: 0.8618 (m-10) REVERT: D 551 LYS cc_start: 0.8200 (tppp) cc_final: 0.7937 (tppp) REVERT: D 556 TYR cc_start: 0.8250 (p90) cc_final: 0.7983 (p90) REVERT: D 563 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8309 (ttpt) REVERT: D 599 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7439 (mtt-85) REVERT: D 642 ASN cc_start: 0.8237 (t0) cc_final: 0.7840 (t0) REVERT: D 661 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6969 (tpt170) REVERT: D 687 ASN cc_start: 0.8550 (t0) cc_final: 0.8349 (t0) REVERT: D 699 LYS cc_start: 0.9166 (tptm) cc_final: 0.8951 (tppp) REVERT: D 715 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7855 (ttp-170) REVERT: D 717 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 723 GLU cc_start: 0.7449 (mp0) cc_final: 0.6880 (mp0) REVERT: D 751 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7249 (tm-30) REVERT: D 752 LYS cc_start: 0.8775 (tptp) cc_final: 0.8351 (tptp) REVERT: D 755 LYS cc_start: 0.8729 (tttt) cc_final: 0.8421 (tptt) REVERT: D 770 GLU cc_start: 0.7690 (tp30) cc_final: 0.6855 (tp30) REVERT: D 774 LEU cc_start: 0.8793 (mm) cc_final: 0.8217 (mm) REVERT: E 297 ARG cc_start: 0.7190 (tpt90) cc_final: 0.6625 (tpt90) REVERT: E 308 LEU cc_start: 0.8572 (mp) cc_final: 0.8308 (mp) REVERT: E 444 TYR cc_start: 0.8383 (t80) cc_final: 0.8039 (t80) REVERT: E 448 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8000 (ttpt) REVERT: E 463 GLU cc_start: 0.8374 (tp30) cc_final: 0.8152 (tp30) REVERT: E 484 LEU cc_start: 0.7891 (mp) cc_final: 0.7610 (tp) REVERT: E 488 LEU cc_start: 0.8755 (tt) cc_final: 0.7928 (tp) REVERT: E 492 GLU cc_start: 0.7604 (mp0) cc_final: 0.7290 (mp0) REVERT: E 498 ILE cc_start: 0.7837 (tt) cc_final: 0.7578 (tt) REVERT: E 514 TYR cc_start: 0.8555 (m-10) cc_final: 0.8264 (m-10) REVERT: E 530 GLU cc_start: 0.7506 (tt0) cc_final: 0.7134 (tt0) REVERT: E 556 TYR cc_start: 0.8234 (p90) cc_final: 0.8029 (p90) REVERT: E 579 LEU cc_start: 0.8544 (mm) cc_final: 0.8121 (mm) REVERT: E 600 GLU cc_start: 0.7817 (pp20) cc_final: 0.7345 (pp20) REVERT: E 619 ASP cc_start: 0.7938 (m-30) cc_final: 0.7458 (m-30) REVERT: E 638 THR cc_start: 0.8568 (t) cc_final: 0.8291 (p) REVERT: E 642 ASN cc_start: 0.8417 (t0) cc_final: 0.8112 (t0) REVERT: E 695 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8375 (tptp) REVERT: E 696 CYS cc_start: 0.8074 (t) cc_final: 0.7796 (t) REVERT: E 715 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7586 (ttp80) REVERT: E 723 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7705 (mm-30) REVERT: E 751 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 752 LYS cc_start: 0.8883 (tmtt) cc_final: 0.8436 (ttmm) REVERT: E 771 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 308 LEU cc_start: 0.8517 (mp) cc_final: 0.8240 (mp) REVERT: F 310 ILE cc_start: 0.8652 (mt) cc_final: 0.8434 (mm) REVERT: F 333 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6979 (tm-30) REVERT: F 393 ASN cc_start: 0.8452 (m-40) cc_final: 0.8219 (m-40) REVERT: F 425 LYS cc_start: 0.8627 (mttm) cc_final: 0.8278 (mmmm) REVERT: F 448 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8180 (ttmm) REVERT: F 468 THR cc_start: 0.8527 (m) cc_final: 0.8146 (p) REVERT: F 485 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7934 (mmtt) REVERT: F 488 LEU cc_start: 0.8071 (tt) cc_final: 0.7702 (tt) REVERT: F 489 LYS cc_start: 0.8113 (mppt) cc_final: 0.7892 (mppt) REVERT: F 492 GLU cc_start: 0.7460 (mp0) cc_final: 0.7035 (mp0) REVERT: F 499 ARG cc_start: 0.7827 (tpm170) cc_final: 0.6561 (tpt170) REVERT: F 523 GLU cc_start: 0.7457 (tp30) cc_final: 0.7041 (tp30) REVERT: F 536 LEU cc_start: 0.8683 (mm) cc_final: 0.8482 (mt) REVERT: F 540 GLU cc_start: 0.7311 (pp20) cc_final: 0.7025 (pp20) REVERT: F 568 LYS cc_start: 0.8623 (mttt) cc_final: 0.8418 (mtpt) REVERT: F 595 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7763 (mm-30) REVERT: F 600 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7648 (tm-30) REVERT: F 642 ASN cc_start: 0.8445 (t0) cc_final: 0.8143 (t0) REVERT: F 661 ARG cc_start: 0.7417 (tpt170) cc_final: 0.6451 (tpt170) REVERT: F 663 ASP cc_start: 0.8284 (p0) cc_final: 0.7963 (p0) REVERT: F 676 ASP cc_start: 0.7657 (p0) cc_final: 0.7238 (p0) REVERT: F 687 ASN cc_start: 0.8797 (t0) cc_final: 0.8553 (t0) REVERT: F 691 GLU cc_start: 0.8205 (tp30) cc_final: 0.7797 (tp30) REVERT: F 729 GLN cc_start: 0.8541 (mt0) cc_final: 0.8236 (mt0) REVERT: F 730 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7670 (mm-30) REVERT: F 751 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6988 (tm-30) REVERT: F 752 LYS cc_start: 0.8627 (tptp) cc_final: 0.8339 (tptp) REVERT: F 754 PHE cc_start: 0.8595 (t80) cc_final: 0.8376 (t80) REVERT: F 770 GLU cc_start: 0.7541 (tp30) cc_final: 0.6991 (tp30) outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.4486 time to fit residues: 672.7116 Evaluate side-chains 954 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 294 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 GLN D 267 GLN E 729 GLN F 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25782 Z= 0.236 Angle : 0.692 10.800 34986 Z= 0.349 Chirality : 0.045 0.237 4020 Planarity : 0.006 0.102 4488 Dihedral : 13.509 173.269 3816 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.63 % Allowed : 12.74 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.35 (0.15), residues: 3240 helix: 0.11 (0.13), residues: 1578 sheet: 0.24 (0.29), residues: 354 loop : -0.63 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 515 HIS 0.006 0.001 HIS A 266 PHE 0.030 0.002 PHE D 587 TYR 0.020 0.002 TYR C 452 ARG 0.007 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 980 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 VAL cc_start: 0.8861 (t) cc_final: 0.8481 (p) REVERT: A 333 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 335 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7765 (mtp-110) REVERT: A 429 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7593 (mmm-85) REVERT: A 443 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8223 (mmmm) REVERT: A 444 TYR cc_start: 0.8499 (t80) cc_final: 0.7984 (t80) REVERT: A 448 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7924 (mttt) REVERT: A 485 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7942 (mmtt) REVERT: A 495 MET cc_start: 0.8141 (mtp) cc_final: 0.7864 (ttm) REVERT: A 499 ARG cc_start: 0.6595 (tpm170) cc_final: 0.4364 (mmm160) REVERT: A 512 LYS cc_start: 0.8455 (tttp) cc_final: 0.8140 (tttp) REVERT: A 523 GLU cc_start: 0.7383 (tp30) cc_final: 0.6929 (tp30) REVERT: A 540 GLU cc_start: 0.7293 (pp20) cc_final: 0.6979 (pp20) REVERT: A 548 SER cc_start: 0.8742 (m) cc_final: 0.8137 (p) REVERT: A 556 TYR cc_start: 0.8161 (p90) cc_final: 0.7893 (p90) REVERT: A 595 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 663 ASP cc_start: 0.7577 (p0) cc_final: 0.7301 (p0) REVERT: A 664 GLU cc_start: 0.7782 (pt0) cc_final: 0.7445 (pt0) REVERT: A 691 GLU cc_start: 0.8154 (tp30) cc_final: 0.7675 (mm-30) REVERT: A 695 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8378 (tptp) REVERT: A 717 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 737 MET cc_start: 0.6485 (ttm) cc_final: 0.6271 (ttm) REVERT: A 751 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6932 (tm-30) REVERT: A 752 LYS cc_start: 0.8722 (tttm) cc_final: 0.8357 (ttmm) REVERT: B 252 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7990 (ttmm) REVERT: B 262 GLU cc_start: 0.7910 (tp30) cc_final: 0.7693 (tp30) REVERT: B 308 LEU cc_start: 0.8547 (mp) cc_final: 0.7964 (mp) REVERT: B 328 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7840 (ttm110) REVERT: B 333 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 391 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7416 (ptt-90) REVERT: B 421 ASP cc_start: 0.8160 (t0) cc_final: 0.7873 (t0) REVERT: B 463 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7912 (mm-30) REVERT: B 485 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8109 (mmtp) REVERT: B 488 LEU cc_start: 0.8414 (tp) cc_final: 0.7681 (tp) REVERT: B 490 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (t0) REVERT: B 497 ASP cc_start: 0.7333 (t0) cc_final: 0.6889 (t0) REVERT: B 525 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8101 (mmtt) REVERT: B 530 GLU cc_start: 0.7951 (tt0) cc_final: 0.7411 (tt0) REVERT: B 540 GLU cc_start: 0.7479 (pp20) cc_final: 0.7246 (pp20) REVERT: B 572 THR cc_start: 0.8389 (m) cc_final: 0.8173 (m) REVERT: B 600 GLU cc_start: 0.7632 (pp20) cc_final: 0.7187 (pp20) REVERT: B 619 ASP cc_start: 0.7968 (m-30) cc_final: 0.7609 (m-30) REVERT: B 638 THR cc_start: 0.8595 (t) cc_final: 0.8293 (p) REVERT: B 642 ASN cc_start: 0.8451 (t0) cc_final: 0.8133 (t0) REVERT: B 661 ARG cc_start: 0.7410 (tpt170) cc_final: 0.7077 (tpm170) REVERT: B 695 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8288 (tptm) REVERT: B 696 CYS cc_start: 0.8085 (t) cc_final: 0.7795 (t) REVERT: B 717 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 751 GLU cc_start: 0.7697 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 752 LYS cc_start: 0.8779 (tttm) cc_final: 0.8368 (ttmm) REVERT: B 755 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8371 (ttmm) REVERT: C 252 LYS cc_start: 0.8370 (mttm) cc_final: 0.8162 (mttm) REVERT: C 255 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 262 GLU cc_start: 0.7947 (tp30) cc_final: 0.7686 (tp30) REVERT: C 308 LEU cc_start: 0.8579 (mp) cc_final: 0.8131 (mp) REVERT: C 333 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6662 (tm-30) REVERT: C 382 LYS cc_start: 0.7113 (mtmt) cc_final: 0.6791 (mtmm) REVERT: C 391 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7063 (ptt90) REVERT: C 393 ASN cc_start: 0.8386 (m-40) cc_final: 0.8128 (m-40) REVERT: C 406 ASP cc_start: 0.6915 (t0) cc_final: 0.6376 (m-30) REVERT: C 420 PHE cc_start: 0.8882 (t80) cc_final: 0.8671 (t80) REVERT: C 425 LYS cc_start: 0.8558 (mttt) cc_final: 0.8317 (mttt) REVERT: C 443 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8429 (mmtp) REVERT: C 463 GLU cc_start: 0.8184 (tp30) cc_final: 0.7959 (tp30) REVERT: C 467 LYS cc_start: 0.8431 (mttm) cc_final: 0.8213 (mmtp) REVERT: C 490 ASP cc_start: 0.7992 (t0) cc_final: 0.7368 (t0) REVERT: C 493 SER cc_start: 0.8791 (t) cc_final: 0.8267 (p) REVERT: C 512 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7942 (mmmt) REVERT: C 522 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7364 (mm-30) REVERT: C 540 GLU cc_start: 0.7530 (pp20) cc_final: 0.7259 (pp20) REVERT: C 572 THR cc_start: 0.8456 (m) cc_final: 0.8244 (m) REVERT: C 595 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 599 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7702 (ttm-80) REVERT: C 600 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7410 (tm-30) REVERT: C 661 ARG cc_start: 0.7236 (tpt170) cc_final: 0.6649 (tpt170) REVERT: C 663 ASP cc_start: 0.8061 (p0) cc_final: 0.7785 (p0) REVERT: C 671 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7819 (ttm-80) REVERT: C 701 ASN cc_start: 0.7790 (m-40) cc_final: 0.6760 (m-40) REVERT: C 708 ASP cc_start: 0.8402 (p0) cc_final: 0.8069 (p0) REVERT: C 730 GLU cc_start: 0.7943 (tp30) cc_final: 0.7696 (tp30) REVERT: C 751 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 755 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8202 (tmtt) REVERT: C 771 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6985 (pp20) REVERT: D 247 VAL cc_start: 0.8731 (t) cc_final: 0.8417 (p) REVERT: D 252 LYS cc_start: 0.8266 (tppp) cc_final: 0.7945 (tppp) REVERT: D 254 ILE cc_start: 0.8887 (mm) cc_final: 0.8601 (mt) REVERT: D 277 SER cc_start: 0.8053 (t) cc_final: 0.7511 (p) REVERT: D 297 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6380 (mmm160) REVERT: D 301 ASN cc_start: 0.7429 (m110) cc_final: 0.7032 (m110) REVERT: D 328 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8131 (ttm110) REVERT: D 333 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6495 (tm-30) REVERT: D 374 MET cc_start: 0.7935 (tpt) cc_final: 0.7632 (tpp) REVERT: D 415 ASP cc_start: 0.7242 (p0) cc_final: 0.7010 (p0) REVERT: D 426 GLN cc_start: 0.8333 (tp40) cc_final: 0.7915 (tp40) REVERT: D 443 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8341 (mmtp) REVERT: D 444 TYR cc_start: 0.8383 (t80) cc_final: 0.8155 (t80) REVERT: D 448 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8230 (ttmm) REVERT: D 497 ASP cc_start: 0.7744 (t0) cc_final: 0.7509 (t0) REVERT: D 510 MET cc_start: 0.7669 (mtt) cc_final: 0.7469 (mtt) REVERT: D 512 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7812 (ttmm) REVERT: D 513 VAL cc_start: 0.8695 (m) cc_final: 0.8343 (p) REVERT: D 517 ASP cc_start: 0.8520 (m-30) cc_final: 0.8306 (m-30) REVERT: D 523 GLU cc_start: 0.7493 (tp30) cc_final: 0.6831 (tp30) REVERT: D 525 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8412 (mmmm) REVERT: D 530 GLU cc_start: 0.7601 (tt0) cc_final: 0.7352 (tt0) REVERT: D 556 TYR cc_start: 0.8046 (p90) cc_final: 0.7835 (p90) REVERT: D 599 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7167 (mtt-85) REVERT: D 604 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8262 (ttmt) REVERT: D 638 THR cc_start: 0.8600 (t) cc_final: 0.8309 (p) REVERT: D 642 ASN cc_start: 0.8256 (t0) cc_final: 0.7855 (t0) REVERT: D 661 ARG cc_start: 0.7210 (tpt170) cc_final: 0.7007 (tpt170) REVERT: D 690 LEU cc_start: 0.9206 (tp) cc_final: 0.8999 (tt) REVERT: D 699 LYS cc_start: 0.9202 (tptm) cc_final: 0.8829 (tppp) REVERT: D 717 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 723 GLU cc_start: 0.7433 (mp0) cc_final: 0.6881 (mp0) REVERT: D 751 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7152 (tm-30) REVERT: D 752 LYS cc_start: 0.8763 (tptp) cc_final: 0.8292 (tptp) REVERT: D 755 LYS cc_start: 0.8524 (tttt) cc_final: 0.8259 (tptp) REVERT: D 770 GLU cc_start: 0.7653 (tp30) cc_final: 0.6800 (tp30) REVERT: E 277 SER cc_start: 0.7529 (t) cc_final: 0.7192 (p) REVERT: E 297 ARG cc_start: 0.7211 (tpt90) cc_final: 0.6642 (tpt90) REVERT: E 443 LYS cc_start: 0.8843 (tppt) cc_final: 0.8349 (tppt) REVERT: E 444 TYR cc_start: 0.8403 (t80) cc_final: 0.7951 (t80) REVERT: E 448 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8014 (ttmt) REVERT: E 453 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8688 (m) REVERT: E 484 LEU cc_start: 0.8073 (mp) cc_final: 0.7715 (tt) REVERT: E 488 LEU cc_start: 0.8751 (tt) cc_final: 0.7927 (tt) REVERT: E 490 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7523 (t0) REVERT: E 492 GLU cc_start: 0.7697 (mp0) cc_final: 0.7177 (mp0) REVERT: E 498 ILE cc_start: 0.7615 (tt) cc_final: 0.7413 (tt) REVERT: E 512 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7918 (ttpt) REVERT: E 600 GLU cc_start: 0.7721 (pp20) cc_final: 0.7227 (pp20) REVERT: E 619 ASP cc_start: 0.7774 (m-30) cc_final: 0.7166 (m-30) REVERT: E 642 ASN cc_start: 0.8520 (t0) cc_final: 0.8272 (t0) REVERT: E 664 GLU cc_start: 0.7819 (tt0) cc_final: 0.7494 (tt0) REVERT: E 691 GLU cc_start: 0.8262 (tp30) cc_final: 0.7904 (tp30) REVERT: E 715 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7655 (ttp80) REVERT: E 723 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7646 (mm-30) REVERT: E 730 GLU cc_start: 0.7986 (tp30) cc_final: 0.7785 (tp30) REVERT: E 745 VAL cc_start: 0.8370 (t) cc_final: 0.7830 (m) REVERT: E 752 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8591 (ttmm) REVERT: E 771 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7477 (tm-30) REVERT: F 310 ILE cc_start: 0.8665 (mt) cc_final: 0.8464 (mm) REVERT: F 393 ASN cc_start: 0.8438 (m-40) cc_final: 0.8199 (m-40) REVERT: F 408 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6677 (mt-10) REVERT: F 463 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7824 (mm-30) REVERT: F 485 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7774 (mmtt) REVERT: F 490 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7526 (t0) REVERT: F 499 ARG cc_start: 0.7580 (tpm170) cc_final: 0.6719 (tpt170) REVERT: F 523 GLU cc_start: 0.7403 (tp30) cc_final: 0.6935 (tp30) REVERT: F 536 LEU cc_start: 0.8678 (mm) cc_final: 0.8390 (tp) REVERT: F 556 TYR cc_start: 0.8125 (p90) cc_final: 0.7910 (p90) REVERT: F 573 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6726 (tm-30) REVERT: F 595 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7662 (mm-30) REVERT: F 599 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: F 621 LEU cc_start: 0.8017 (mt) cc_final: 0.7445 (mp) REVERT: F 642 ASN cc_start: 0.8454 (t0) cc_final: 0.8131 (t0) REVERT: F 661 ARG cc_start: 0.7462 (tpt170) cc_final: 0.6392 (tpt170) REVERT: F 663 ASP cc_start: 0.8225 (p0) cc_final: 0.7828 (p0) REVERT: F 664 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 687 ASN cc_start: 0.8728 (t0) cc_final: 0.8484 (t0) REVERT: F 691 GLU cc_start: 0.8147 (tp30) cc_final: 0.7569 (tp30) REVERT: F 729 GLN cc_start: 0.8447 (mt0) cc_final: 0.8120 (mt0) REVERT: F 751 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6927 (tm-30) REVERT: F 752 LYS cc_start: 0.8584 (tptp) cc_final: 0.8288 (tptp) REVERT: F 754 PHE cc_start: 0.8470 (t80) cc_final: 0.8249 (t80) REVERT: F 771 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7354 (pp20) outliers start: 44 outliers final: 19 residues processed: 991 average time/residue: 0.4925 time to fit residues: 704.6731 Evaluate side-chains 942 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 918 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 619 ASP Chi-restraints excluded: chain D residue 701 ASN Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 634 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 292 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 GLN C 687 ASN D 393 ASN D 687 ASN E 729 GLN F 701 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25782 Z= 0.237 Angle : 0.663 10.934 34986 Z= 0.332 Chirality : 0.044 0.226 4020 Planarity : 0.006 0.077 4488 Dihedral : 13.131 169.574 3816 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.59 % Allowed : 16.07 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.25 (0.15), residues: 3240 helix: 0.14 (0.13), residues: 1608 sheet: 0.31 (0.29), residues: 366 loop : -0.53 (0.19), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 515 HIS 0.025 0.001 HIS B 285 PHE 0.035 0.002 PHE B 507 TYR 0.027 0.002 TYR B 556 ARG 0.009 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 959 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7687 (tp30) cc_final: 0.7252 (tm-30) REVERT: A 333 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 335 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7731 (mtp-110) REVERT: A 429 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7692 (mmm-85) REVERT: A 443 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8233 (mmmm) REVERT: A 444 TYR cc_start: 0.8467 (t80) cc_final: 0.8021 (t80) REVERT: A 448 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7817 (mttt) REVERT: A 495 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7956 (ttm) REVERT: A 512 LYS cc_start: 0.8478 (tttp) cc_final: 0.8196 (tttp) REVERT: A 514 TYR cc_start: 0.8498 (m-10) cc_final: 0.8167 (m-80) REVERT: A 523 GLU cc_start: 0.7440 (tp30) cc_final: 0.6961 (tp30) REVERT: A 540 GLU cc_start: 0.7309 (pp20) cc_final: 0.6982 (pp20) REVERT: A 548 SER cc_start: 0.8728 (m) cc_final: 0.8460 (p) REVERT: A 556 TYR cc_start: 0.8192 (p90) cc_final: 0.7895 (p90) REVERT: A 572 THR cc_start: 0.8408 (m) cc_final: 0.8092 (p) REVERT: A 595 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7699 (mp0) REVERT: A 661 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7079 (mmm160) REVERT: A 663 ASP cc_start: 0.7667 (p0) cc_final: 0.6428 (p0) REVERT: A 664 GLU cc_start: 0.7768 (pt0) cc_final: 0.7496 (pt0) REVERT: A 695 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8363 (tptp) REVERT: A 717 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 751 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 752 LYS cc_start: 0.8787 (tttm) cc_final: 0.8425 (ttmm) REVERT: A 755 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8337 (ttmt) REVERT: B 311 ASN cc_start: 0.7627 (t0) cc_final: 0.7378 (t0) REVERT: B 328 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7843 (ttm110) REVERT: B 333 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6638 (tm-30) REVERT: B 391 ARG cc_start: 0.7928 (ptt-90) cc_final: 0.7132 (ptt-90) REVERT: B 421 ASP cc_start: 0.8135 (t0) cc_final: 0.7818 (t0) REVERT: B 430 MET cc_start: 0.7523 (ptt) cc_final: 0.7279 (ptt) REVERT: B 434 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7487 (mmm-85) REVERT: B 490 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7509 (t0) REVERT: B 497 ASP cc_start: 0.7389 (t0) cc_final: 0.6897 (t0) REVERT: B 525 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8046 (mmtp) REVERT: B 540 GLU cc_start: 0.7548 (pp20) cc_final: 0.7310 (pp20) REVERT: B 585 GLU cc_start: 0.7404 (pt0) cc_final: 0.7159 (pp20) REVERT: B 600 GLU cc_start: 0.7622 (pp20) cc_final: 0.7132 (pp20) REVERT: B 617 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7354 (mp0) REVERT: B 638 THR cc_start: 0.8507 (t) cc_final: 0.8261 (p) REVERT: B 642 ASN cc_start: 0.8434 (t0) cc_final: 0.8069 (t0) REVERT: B 661 ARG cc_start: 0.7576 (tpt170) cc_final: 0.7333 (tpm170) REVERT: B 678 HIS cc_start: 0.7686 (m170) cc_final: 0.7411 (m170) REVERT: B 695 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8282 (tptm) REVERT: B 696 CYS cc_start: 0.8085 (t) cc_final: 0.7809 (t) REVERT: B 751 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7283 (tp30) REVERT: B 752 LYS cc_start: 0.8805 (tttm) cc_final: 0.8575 (ttmm) REVERT: C 255 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 308 LEU cc_start: 0.8519 (mp) cc_final: 0.8316 (mp) REVERT: C 333 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6716 (tm-30) REVERT: C 382 LYS cc_start: 0.7061 (mtmt) cc_final: 0.6788 (mtmm) REVERT: C 393 ASN cc_start: 0.8425 (m-40) cc_final: 0.8161 (m-40) REVERT: C 425 LYS cc_start: 0.8618 (mttt) cc_final: 0.8341 (mttt) REVERT: C 443 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8458 (mmtp) REVERT: C 467 LYS cc_start: 0.8460 (mttm) cc_final: 0.8105 (mmtp) REVERT: C 468 THR cc_start: 0.8476 (m) cc_final: 0.8114 (p) REVERT: C 484 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8296 (mm) REVERT: C 488 LEU cc_start: 0.8055 (tt) cc_final: 0.7842 (tp) REVERT: C 490 ASP cc_start: 0.7909 (t0) cc_final: 0.7351 (t0) REVERT: C 493 SER cc_start: 0.8873 (t) cc_final: 0.8266 (p) REVERT: C 512 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7946 (mmmt) REVERT: C 522 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7396 (mm-30) REVERT: C 540 GLU cc_start: 0.7544 (pp20) cc_final: 0.7255 (pp20) REVERT: C 595 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7879 (mt-10) REVERT: C 599 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7705 (ttm-80) REVERT: C 600 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7322 (tm-30) REVERT: C 661 ARG cc_start: 0.7321 (tpt170) cc_final: 0.6891 (tpt170) REVERT: C 715 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7677 (ttp80) REVERT: C 717 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 730 GLU cc_start: 0.7921 (tp30) cc_final: 0.7720 (tp30) REVERT: C 751 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 755 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8335 (tmtt) REVERT: C 771 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7139 (pp20) REVERT: D 247 VAL cc_start: 0.8721 (t) cc_final: 0.8367 (p) REVERT: D 252 LYS cc_start: 0.8265 (tppp) cc_final: 0.7940 (tppp) REVERT: D 292 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8389 (mtmm) REVERT: D 301 ASN cc_start: 0.7468 (m110) cc_final: 0.7148 (m110) REVERT: D 328 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8058 (ttm110) REVERT: D 333 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6582 (tm-30) REVERT: D 374 MET cc_start: 0.7920 (tpt) cc_final: 0.7643 (tpp) REVERT: D 423 LEU cc_start: 0.9134 (mt) cc_final: 0.8925 (mt) REVERT: D 426 GLN cc_start: 0.8405 (tp40) cc_final: 0.7935 (tp40) REVERT: D 443 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8312 (mmtp) REVERT: D 444 TYR cc_start: 0.8341 (t80) cc_final: 0.7974 (t80) REVERT: D 512 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7862 (ttmm) REVERT: D 523 GLU cc_start: 0.7508 (tp30) cc_final: 0.6860 (tp30) REVERT: D 527 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8097 (mtpp) REVERT: D 556 TYR cc_start: 0.8056 (p90) cc_final: 0.7815 (p90) REVERT: D 600 GLU cc_start: 0.7503 (pp20) cc_final: 0.7085 (pp20) REVERT: D 642 ASN cc_start: 0.8277 (t0) cc_final: 0.7888 (t0) REVERT: D 675 LEU cc_start: 0.8588 (tp) cc_final: 0.8351 (mt) REVERT: D 690 LEU cc_start: 0.9194 (tp) cc_final: 0.8951 (tt) REVERT: D 699 LYS cc_start: 0.9203 (tptm) cc_final: 0.8821 (tppp) REVERT: D 717 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 723 GLU cc_start: 0.7435 (mp0) cc_final: 0.6894 (mp0) REVERT: D 737 MET cc_start: 0.6620 (ttm) cc_final: 0.6366 (ttm) REVERT: D 751 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7138 (tm-30) REVERT: D 755 LYS cc_start: 0.8527 (tttt) cc_final: 0.8245 (tptp) REVERT: E 253 GLU cc_start: 0.7646 (pm20) cc_final: 0.7426 (mp0) REVERT: E 292 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8237 (mttm) REVERT: E 297 ARG cc_start: 0.7253 (tpt90) cc_final: 0.6996 (tpt90) REVERT: E 443 LYS cc_start: 0.8795 (tppt) cc_final: 0.8367 (tppt) REVERT: E 444 TYR cc_start: 0.8364 (t80) cc_final: 0.7960 (t80) REVERT: E 448 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8056 (ttmt) REVERT: E 453 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8705 (m) REVERT: E 488 LEU cc_start: 0.8815 (tt) cc_final: 0.7996 (tt) REVERT: E 490 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7595 (t0) REVERT: E 492 GLU cc_start: 0.7745 (mp0) cc_final: 0.7220 (mp0) REVERT: E 498 ILE cc_start: 0.7734 (tt) cc_final: 0.7506 (tt) REVERT: E 512 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7925 (ttpt) REVERT: E 530 GLU cc_start: 0.7341 (tt0) cc_final: 0.7048 (tt0) REVERT: E 595 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7790 (mm-30) REVERT: E 600 GLU cc_start: 0.7711 (pp20) cc_final: 0.7245 (pp20) REVERT: E 619 ASP cc_start: 0.7819 (m-30) cc_final: 0.7369 (m-30) REVERT: E 642 ASN cc_start: 0.8538 (t0) cc_final: 0.8267 (t0) REVERT: E 664 GLU cc_start: 0.7834 (tt0) cc_final: 0.7446 (tt0) REVERT: E 691 GLU cc_start: 0.8236 (tp30) cc_final: 0.7998 (tp30) REVERT: E 715 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7661 (ttp80) REVERT: E 723 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7637 (mm-30) REVERT: E 745 VAL cc_start: 0.8436 (t) cc_final: 0.7969 (m) REVERT: E 752 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8489 (tmtt) REVERT: E 761 ILE cc_start: 0.8824 (mm) cc_final: 0.8606 (mt) REVERT: F 292 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8474 (mttp) REVERT: F 311 ASN cc_start: 0.7757 (t0) cc_final: 0.7384 (t0) REVERT: F 335 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7773 (mtp-110) REVERT: F 374 MET cc_start: 0.7715 (tpt) cc_final: 0.7460 (tpt) REVERT: F 393 ASN cc_start: 0.8535 (m-40) cc_final: 0.8289 (m-40) REVERT: F 444 TYR cc_start: 0.8549 (t80) cc_final: 0.7827 (t80) REVERT: F 485 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7748 (mmtt) REVERT: F 490 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7527 (t0) REVERT: F 492 GLU cc_start: 0.7630 (mp0) cc_final: 0.6967 (mp0) REVERT: F 499 ARG cc_start: 0.7425 (tpm170) cc_final: 0.6280 (tpt170) REVERT: F 536 LEU cc_start: 0.8710 (mm) cc_final: 0.8399 (tp) REVERT: F 621 LEU cc_start: 0.8050 (mt) cc_final: 0.7445 (mp) REVERT: F 642 ASN cc_start: 0.8343 (t0) cc_final: 0.8051 (t0) REVERT: F 661 ARG cc_start: 0.7388 (tpt170) cc_final: 0.6445 (tpt170) REVERT: F 663 ASP cc_start: 0.8173 (p0) cc_final: 0.7858 (p0) REVERT: F 687 ASN cc_start: 0.8727 (t0) cc_final: 0.8498 (t0) REVERT: F 751 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7248 (tp30) REVERT: F 752 LYS cc_start: 0.8623 (tptp) cc_final: 0.8394 (tptp) outliers start: 70 outliers final: 40 residues processed: 980 average time/residue: 0.4786 time to fit residues: 671.1617 Evaluate side-chains 947 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 900 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 694 LYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 762 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 618 ILE Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 197 optimal weight: 0.2980 chunk 295 optimal weight: 0.9990 chunk 313 optimal weight: 0.6980 chunk 154 optimal weight: 0.3980 chunk 280 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN E 729 GLN F 426 GLN F 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25782 Z= 0.179 Angle : 0.632 12.186 34986 Z= 0.314 Chirality : 0.043 0.217 4020 Planarity : 0.005 0.076 4488 Dihedral : 12.716 159.578 3816 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.33 % Allowed : 18.44 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.06 (0.15), residues: 3240 helix: 0.35 (0.13), residues: 1572 sheet: 0.26 (0.29), residues: 384 loop : -0.47 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 515 HIS 0.014 0.001 HIS B 285 PHE 0.037 0.002 PHE D 587 TYR 0.027 0.002 TYR B 556 ARG 0.009 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 934 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7608 (tp30) cc_final: 0.7243 (tm-30) REVERT: A 251 ASP cc_start: 0.7534 (m-30) cc_final: 0.7151 (m-30) REVERT: A 252 LYS cc_start: 0.8127 (tppp) cc_final: 0.7719 (tppp) REVERT: A 333 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 335 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7670 (mtp-110) REVERT: A 429 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7578 (mmm-85) REVERT: A 443 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8440 (tppt) REVERT: A 444 TYR cc_start: 0.8393 (t80) cc_final: 0.7924 (t80) REVERT: A 448 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7818 (mttt) REVERT: A 485 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7895 (mmtt) REVERT: A 492 GLU cc_start: 0.7906 (mp0) cc_final: 0.7532 (mp0) REVERT: A 512 LYS cc_start: 0.8442 (tttp) cc_final: 0.8166 (tttp) REVERT: A 523 GLU cc_start: 0.7418 (tp30) cc_final: 0.6944 (tp30) REVERT: A 540 GLU cc_start: 0.7280 (pp20) cc_final: 0.6997 (pp20) REVERT: A 548 SER cc_start: 0.8704 (m) cc_final: 0.8448 (p) REVERT: A 556 TYR cc_start: 0.8047 (p90) cc_final: 0.7782 (p90) REVERT: A 572 THR cc_start: 0.8315 (m) cc_final: 0.8050 (p) REVERT: A 595 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7696 (mp0) REVERT: A 663 ASP cc_start: 0.7633 (p0) cc_final: 0.7126 (p0) REVERT: A 664 GLU cc_start: 0.7714 (pt0) cc_final: 0.7467 (pt0) REVERT: A 695 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8362 (tptp) REVERT: A 717 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 751 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6852 (tm-30) REVERT: A 752 LYS cc_start: 0.8767 (tttm) cc_final: 0.8402 (ttmm) REVERT: A 755 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8302 (ttmt) REVERT: B 301 ASN cc_start: 0.8154 (t0) cc_final: 0.7898 (t0) REVERT: B 311 ASN cc_start: 0.7610 (t0) cc_final: 0.7378 (t0) REVERT: B 328 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7824 (ttm110) REVERT: B 391 ARG cc_start: 0.7952 (ptt-90) cc_final: 0.7426 (ptt-90) REVERT: B 421 ASP cc_start: 0.8067 (t0) cc_final: 0.7783 (t0) REVERT: B 444 TYR cc_start: 0.8145 (t80) cc_final: 0.7728 (t80) REVERT: B 448 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8088 (ptpt) REVERT: B 486 VAL cc_start: 0.8879 (p) cc_final: 0.8543 (m) REVERT: B 490 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7667 (t0) REVERT: B 497 ASP cc_start: 0.7474 (t0) cc_final: 0.6976 (t0) REVERT: B 525 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8115 (mmtp) REVERT: B 585 GLU cc_start: 0.7415 (pt0) cc_final: 0.6993 (pp20) REVERT: B 600 GLU cc_start: 0.7538 (pp20) cc_final: 0.7164 (pp20) REVERT: B 617 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7424 (mp0) REVERT: B 638 THR cc_start: 0.8449 (t) cc_final: 0.8222 (p) REVERT: B 642 ASN cc_start: 0.8374 (t0) cc_final: 0.8009 (t0) REVERT: B 661 ARG cc_start: 0.7504 (tpt170) cc_final: 0.7182 (tpm170) REVERT: B 678 HIS cc_start: 0.7672 (m170) cc_final: 0.7457 (m170) REVERT: B 689 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: B 695 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8263 (tptm) REVERT: B 696 CYS cc_start: 0.8068 (t) cc_final: 0.7805 (t) REVERT: B 751 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7447 (tp30) REVERT: B 752 LYS cc_start: 0.8781 (tttm) cc_final: 0.8496 (ttmm) REVERT: B 775 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7636 (ttp80) REVERT: C 255 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7395 (tm-30) REVERT: C 308 LEU cc_start: 0.8455 (mp) cc_final: 0.7971 (mp) REVERT: C 324 GLU cc_start: 0.7623 (mp0) cc_final: 0.6617 (mp0) REVERT: C 333 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6675 (tm-30) REVERT: C 382 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6739 (mtmm) REVERT: C 393 ASN cc_start: 0.8404 (m-40) cc_final: 0.8158 (m-40) REVERT: C 406 ASP cc_start: 0.6938 (t0) cc_final: 0.6477 (m-30) REVERT: C 425 LYS cc_start: 0.8618 (mttt) cc_final: 0.8398 (tppp) REVERT: C 443 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8468 (mmtp) REVERT: C 453 VAL cc_start: 0.8777 (p) cc_final: 0.8392 (m) REVERT: C 463 GLU cc_start: 0.8210 (tp30) cc_final: 0.8004 (tp30) REVERT: C 467 LYS cc_start: 0.8445 (mttm) cc_final: 0.8075 (mmtp) REVERT: C 468 THR cc_start: 0.8496 (m) cc_final: 0.8122 (p) REVERT: C 484 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8244 (mm) REVERT: C 488 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7711 (tp) REVERT: C 490 ASP cc_start: 0.7868 (t0) cc_final: 0.7296 (t0) REVERT: C 493 SER cc_start: 0.8865 (t) cc_final: 0.8280 (p) REVERT: C 512 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7879 (mmmt) REVERT: C 522 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7440 (mm-30) REVERT: C 540 GLU cc_start: 0.7538 (pp20) cc_final: 0.7272 (pp20) REVERT: C 595 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 599 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7681 (mtt-85) REVERT: C 600 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7193 (tm-30) REVERT: C 661 ARG cc_start: 0.7390 (tpt170) cc_final: 0.6727 (tpt170) REVERT: C 715 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7621 (ttp80) REVERT: C 730 GLU cc_start: 0.7954 (tp30) cc_final: 0.7504 (mm-30) REVERT: C 751 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7162 (tm-30) REVERT: C 755 LYS cc_start: 0.8474 (tmtt) cc_final: 0.8238 (tmtt) REVERT: C 761 ILE cc_start: 0.8448 (tt) cc_final: 0.8229 (pt) REVERT: D 252 LYS cc_start: 0.8175 (tppp) cc_final: 0.7793 (tppp) REVERT: D 301 ASN cc_start: 0.7483 (m110) cc_final: 0.7128 (m110) REVERT: D 328 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8014 (ttm110) REVERT: D 333 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6581 (tm-30) REVERT: D 374 MET cc_start: 0.7866 (tpt) cc_final: 0.7594 (tpp) REVERT: D 426 GLN cc_start: 0.8381 (tp40) cc_final: 0.7920 (tp40) REVERT: D 443 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8255 (mmtp) REVERT: D 444 TYR cc_start: 0.8304 (t80) cc_final: 0.7729 (t80) REVERT: D 448 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8033 (mtmt) REVERT: D 522 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 523 GLU cc_start: 0.7484 (tp30) cc_final: 0.6789 (tp30) REVERT: D 527 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8174 (mtpp) REVERT: D 530 GLU cc_start: 0.7653 (tt0) cc_final: 0.7226 (tt0) REVERT: D 537 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: D 556 TYR cc_start: 0.8000 (p90) cc_final: 0.7764 (p90) REVERT: D 600 GLU cc_start: 0.7473 (pp20) cc_final: 0.7045 (pp20) REVERT: D 604 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8358 (ttmt) REVERT: D 642 ASN cc_start: 0.8285 (t0) cc_final: 0.7831 (t0) REVERT: D 675 LEU cc_start: 0.8523 (tp) cc_final: 0.8276 (mt) REVERT: D 690 LEU cc_start: 0.9187 (tp) cc_final: 0.8932 (tt) REVERT: D 699 LYS cc_start: 0.9155 (tptm) cc_final: 0.8807 (tppp) REVERT: D 717 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 737 MET cc_start: 0.6511 (ttm) cc_final: 0.6215 (ttm) REVERT: D 751 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7094 (tm-30) REVERT: D 755 LYS cc_start: 0.8541 (tttt) cc_final: 0.8229 (tptp) REVERT: E 253 GLU cc_start: 0.7612 (pm20) cc_final: 0.7397 (mp0) REVERT: E 292 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8198 (mttm) REVERT: E 297 ARG cc_start: 0.7309 (tpt90) cc_final: 0.7005 (tpt90) REVERT: E 346 GLU cc_start: 0.7262 (mp0) cc_final: 0.6924 (mp0) REVERT: E 425 LYS cc_start: 0.8744 (mttm) cc_final: 0.8430 (mmtp) REVERT: E 430 MET cc_start: 0.7507 (ptt) cc_final: 0.7251 (ptt) REVERT: E 443 LYS cc_start: 0.8779 (tppt) cc_final: 0.8311 (tppt) REVERT: E 444 TYR cc_start: 0.8319 (t80) cc_final: 0.8077 (t80) REVERT: E 448 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8038 (ttmt) REVERT: E 453 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8686 (m) REVERT: E 490 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7683 (t0) REVERT: E 512 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7690 (ttpt) REVERT: E 530 GLU cc_start: 0.7229 (tt0) cc_final: 0.6801 (tt0) REVERT: E 600 GLU cc_start: 0.7675 (pp20) cc_final: 0.7220 (pp20) REVERT: E 617 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7416 (mm-30) REVERT: E 619 ASP cc_start: 0.7822 (m-30) cc_final: 0.7089 (m-30) REVERT: E 642 ASN cc_start: 0.8555 (t0) cc_final: 0.8274 (t0) REVERT: E 661 ARG cc_start: 0.7061 (tpt170) cc_final: 0.6272 (tpt170) REVERT: E 663 ASP cc_start: 0.8283 (p0) cc_final: 0.7921 (p0) REVERT: E 664 GLU cc_start: 0.7818 (tt0) cc_final: 0.7305 (tt0) REVERT: E 745 VAL cc_start: 0.8410 (t) cc_final: 0.7967 (m) REVERT: E 751 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7239 (tp30) REVERT: E 752 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8526 (tmtt) REVERT: E 761 ILE cc_start: 0.8869 (mm) cc_final: 0.8638 (mt) REVERT: E 771 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7139 (pp20) REVERT: F 292 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8232 (mmtm) REVERT: F 311 ASN cc_start: 0.7599 (t0) cc_final: 0.7272 (t0) REVERT: F 374 MET cc_start: 0.7697 (tpt) cc_final: 0.7494 (tpt) REVERT: F 393 ASN cc_start: 0.8547 (m-40) cc_final: 0.8320 (m-40) REVERT: F 443 LYS cc_start: 0.8618 (mmpt) cc_final: 0.8315 (tppt) REVERT: F 444 TYR cc_start: 0.8478 (t80) cc_final: 0.7815 (t80) REVERT: F 468 THR cc_start: 0.8649 (m) cc_final: 0.8102 (p) REVERT: F 485 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7735 (mmtt) REVERT: F 490 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7446 (t0) REVERT: F 499 ARG cc_start: 0.7354 (tpm170) cc_final: 0.6303 (tpt170) REVERT: F 522 GLU cc_start: 0.7552 (tp30) cc_final: 0.7232 (mp0) REVERT: F 536 LEU cc_start: 0.8709 (mm) cc_final: 0.8279 (tp) REVERT: F 540 GLU cc_start: 0.7251 (pp20) cc_final: 0.6925 (pp20) REVERT: F 572 THR cc_start: 0.8340 (m) cc_final: 0.7866 (p) REVERT: F 591 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6546 (p) REVERT: F 595 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7658 (mp0) REVERT: F 642 ASN cc_start: 0.8324 (t0) cc_final: 0.8004 (t0) REVERT: F 661 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6555 (tpt170) REVERT: F 687 ASN cc_start: 0.8664 (t0) cc_final: 0.8458 (t0) REVERT: F 751 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7073 (tp30) REVERT: F 752 LYS cc_start: 0.8579 (tptp) cc_final: 0.8336 (tptp) REVERT: F 771 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7215 (pp20) outliers start: 90 outliers final: 52 residues processed: 963 average time/residue: 0.4644 time to fit residues: 638.8993 Evaluate side-chains 933 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 872 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 694 LYS Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 512 LYS Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 600 GLU Chi-restraints excluded: chain F residue 618 ILE Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** F 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN F 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 25782 Z= 0.329 Angle : 0.689 9.449 34986 Z= 0.343 Chirality : 0.045 0.201 4020 Planarity : 0.005 0.088 4488 Dihedral : 12.767 164.261 3816 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.00 % Allowed : 19.85 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.04 (0.15), residues: 3240 helix: 0.45 (0.13), residues: 1566 sheet: 0.50 (0.30), residues: 366 loop : -0.50 (0.19), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 515 HIS 0.015 0.001 HIS E 285 PHE 0.038 0.002 PHE D 587 TYR 0.023 0.002 TYR D 768 ARG 0.009 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 883 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8247 (tppp) cc_final: 0.7892 (tppp) REVERT: A 253 GLU cc_start: 0.7639 (pm20) cc_final: 0.7236 (pm20) REVERT: A 262 GLU cc_start: 0.7911 (tp30) cc_final: 0.7417 (tm-30) REVERT: A 324 GLU cc_start: 0.6748 (mp0) cc_final: 0.6373 (mp0) REVERT: A 328 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8025 (ttm110) REVERT: A 333 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 335 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7733 (mtp-110) REVERT: A 371 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 423 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8867 (mt) REVERT: A 426 GLN cc_start: 0.8375 (tp40) cc_final: 0.8162 (mm-40) REVERT: A 429 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7708 (mmm-85) REVERT: A 443 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8474 (tppt) REVERT: A 444 TYR cc_start: 0.8480 (t80) cc_final: 0.7988 (t80) REVERT: A 448 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7942 (mttt) REVERT: A 512 LYS cc_start: 0.8450 (tttp) cc_final: 0.8227 (tttp) REVERT: A 523 GLU cc_start: 0.7540 (tp30) cc_final: 0.7062 (tp30) REVERT: A 540 GLU cc_start: 0.7342 (pp20) cc_final: 0.7044 (pp20) REVERT: A 548 SER cc_start: 0.8664 (m) cc_final: 0.8398 (p) REVERT: A 556 TYR cc_start: 0.8232 (p90) cc_final: 0.7903 (p90) REVERT: A 595 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7822 (mm-30) REVERT: A 619 ASP cc_start: 0.8002 (m-30) cc_final: 0.7566 (m-30) REVERT: A 661 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7295 (mmm160) REVERT: A 663 ASP cc_start: 0.7688 (p0) cc_final: 0.7155 (p0) REVERT: A 664 GLU cc_start: 0.7782 (pt0) cc_final: 0.7342 (pt0) REVERT: A 691 GLU cc_start: 0.8099 (tp30) cc_final: 0.7518 (tp30) REVERT: A 695 LYS cc_start: 0.8693 (tmtt) cc_final: 0.8428 (tptp) REVERT: A 717 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 730 GLU cc_start: 0.7855 (tp30) cc_final: 0.7430 (mm-30) REVERT: A 751 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 752 LYS cc_start: 0.8835 (tttm) cc_final: 0.8452 (ttmm) REVERT: A 755 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8349 (ttmt) REVERT: B 301 ASN cc_start: 0.8233 (t0) cc_final: 0.7943 (t0) REVERT: B 311 ASN cc_start: 0.7609 (t0) cc_final: 0.7364 (t0) REVERT: B 328 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7866 (ttm110) REVERT: B 421 ASP cc_start: 0.8146 (t0) cc_final: 0.7835 (t0) REVERT: B 426 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: B 444 TYR cc_start: 0.8173 (t80) cc_final: 0.7653 (t80) REVERT: B 448 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7962 (ptpt) REVERT: B 486 VAL cc_start: 0.8985 (p) cc_final: 0.8654 (m) REVERT: B 490 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7615 (t0) REVERT: B 497 ASP cc_start: 0.7589 (t0) cc_final: 0.7174 (t0) REVERT: B 512 LYS cc_start: 0.8026 (tttm) cc_final: 0.7785 (tttp) REVERT: B 525 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8149 (mmtp) REVERT: B 534 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8893 (tp) REVERT: B 582 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8486 (mmmm) REVERT: B 585 GLU cc_start: 0.7554 (pt0) cc_final: 0.7065 (pp20) REVERT: B 600 GLU cc_start: 0.7780 (pp20) cc_final: 0.7384 (pp20) REVERT: B 617 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7480 (mp0) REVERT: B 638 THR cc_start: 0.8525 (t) cc_final: 0.8295 (p) REVERT: B 642 ASN cc_start: 0.8395 (t0) cc_final: 0.7995 (t0) REVERT: B 661 ARG cc_start: 0.7658 (tpt170) cc_final: 0.7292 (tpt170) REVERT: B 695 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8283 (tptm) REVERT: B 696 CYS cc_start: 0.8110 (t) cc_final: 0.7853 (t) REVERT: B 751 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7524 (tp30) REVERT: B 752 LYS cc_start: 0.8829 (tttm) cc_final: 0.8536 (ttmm) REVERT: C 255 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 292 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8353 (mttp) REVERT: C 324 GLU cc_start: 0.7699 (mp0) cc_final: 0.6807 (mp0) REVERT: C 333 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6700 (tm-30) REVERT: C 382 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6826 (mtmm) REVERT: C 393 ASN cc_start: 0.8497 (m-40) cc_final: 0.8276 (m-40) REVERT: C 425 LYS cc_start: 0.8693 (mttt) cc_final: 0.8413 (mttt) REVERT: C 426 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8143 (mm-40) REVERT: C 443 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8519 (mmtp) REVERT: C 453 VAL cc_start: 0.8908 (p) cc_final: 0.8541 (m) REVERT: C 484 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8207 (mm) REVERT: C 488 LEU cc_start: 0.8094 (tt) cc_final: 0.7552 (tp) REVERT: C 490 ASP cc_start: 0.7926 (t0) cc_final: 0.7276 (t0) REVERT: C 492 GLU cc_start: 0.7820 (mp0) cc_final: 0.7516 (mp0) REVERT: C 493 SER cc_start: 0.8920 (t) cc_final: 0.8587 (p) REVERT: C 512 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8006 (mmmt) REVERT: C 522 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 540 GLU cc_start: 0.7593 (pp20) cc_final: 0.7352 (pp20) REVERT: C 563 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8274 (ttpt) REVERT: C 573 GLU cc_start: 0.7600 (pm20) cc_final: 0.7356 (pm20) REVERT: C 595 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 599 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7718 (mtt-85) REVERT: C 600 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7348 (tm-30) REVERT: C 643 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7808 (mm-30) REVERT: C 661 ARG cc_start: 0.7451 (tpt170) cc_final: 0.6715 (tpt170) REVERT: C 664 GLU cc_start: 0.7894 (tt0) cc_final: 0.7675 (tt0) REVERT: C 696 CYS cc_start: 0.7991 (t) cc_final: 0.7733 (p) REVERT: C 715 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7656 (ttp80) REVERT: C 751 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7208 (tm-30) REVERT: C 755 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8353 (tmtt) REVERT: C 771 GLU cc_start: 0.7589 (pp20) cc_final: 0.7197 (pp20) REVERT: D 252 LYS cc_start: 0.8206 (tppp) cc_final: 0.7867 (tppp) REVERT: D 301 ASN cc_start: 0.7567 (m110) cc_final: 0.7186 (m110) REVERT: D 328 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8044 (ttm110) REVERT: D 333 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6639 (tm-30) REVERT: D 374 MET cc_start: 0.7961 (tpt) cc_final: 0.7695 (tpp) REVERT: D 425 LYS cc_start: 0.8792 (mttm) cc_final: 0.8543 (ttmm) REVERT: D 426 GLN cc_start: 0.8505 (tp40) cc_final: 0.8067 (tp40) REVERT: D 443 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8351 (mmtp) REVERT: D 444 TYR cc_start: 0.8395 (t80) cc_final: 0.7971 (t80) REVERT: D 523 GLU cc_start: 0.7588 (tp30) cc_final: 0.6895 (tp30) REVERT: D 527 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8181 (mtpp) REVERT: D 537 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: D 556 TYR cc_start: 0.8077 (p90) cc_final: 0.7847 (p90) REVERT: D 600 GLU cc_start: 0.7617 (pp20) cc_final: 0.7192 (pp20) REVERT: D 604 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8530 (ttmm) REVERT: D 642 ASN cc_start: 0.8296 (t0) cc_final: 0.7871 (t0) REVERT: D 690 LEU cc_start: 0.9165 (tp) cc_final: 0.8900 (tt) REVERT: D 691 GLU cc_start: 0.8247 (tp30) cc_final: 0.7491 (tp30) REVERT: D 699 LYS cc_start: 0.9160 (tptm) cc_final: 0.8818 (tppp) REVERT: D 717 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 751 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7265 (tp30) REVERT: D 752 LYS cc_start: 0.8797 (tptp) cc_final: 0.8430 (tptp) REVERT: D 755 LYS cc_start: 0.8654 (tttt) cc_final: 0.8326 (tptp) REVERT: D 770 GLU cc_start: 0.8032 (tp30) cc_final: 0.7811 (mm-30) REVERT: E 253 GLU cc_start: 0.7658 (pm20) cc_final: 0.7425 (mp0) REVERT: E 292 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8339 (mttm) REVERT: E 297 ARG cc_start: 0.7398 (tpt90) cc_final: 0.7075 (tpt90) REVERT: E 425 LYS cc_start: 0.8803 (mttm) cc_final: 0.8553 (mmtp) REVERT: E 443 LYS cc_start: 0.8851 (tppt) cc_final: 0.8413 (tppt) REVERT: E 444 TYR cc_start: 0.8407 (t80) cc_final: 0.8034 (t80) REVERT: E 448 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8044 (ttmt) REVERT: E 488 LEU cc_start: 0.8856 (tt) cc_final: 0.8106 (tp) REVERT: E 490 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (t0) REVERT: E 492 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: E 498 ILE cc_start: 0.7843 (tt) cc_final: 0.7526 (pt) REVERT: E 512 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7883 (ttpt) REVERT: E 530 GLU cc_start: 0.7356 (tt0) cc_final: 0.6944 (tt0) REVERT: E 595 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7702 (mm-30) REVERT: E 600 GLU cc_start: 0.7826 (pp20) cc_final: 0.7287 (pp20) REVERT: E 617 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7509 (mm-30) REVERT: E 642 ASN cc_start: 0.8585 (t0) cc_final: 0.8302 (t0) REVERT: E 661 ARG cc_start: 0.7457 (tpt170) cc_final: 0.6929 (tpt170) REVERT: E 696 CYS cc_start: 0.8107 (t) cc_final: 0.7830 (t) REVERT: E 745 VAL cc_start: 0.8520 (t) cc_final: 0.8091 (m) REVERT: E 751 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7366 (tp30) REVERT: E 752 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8558 (tmtt) REVERT: E 754 PHE cc_start: 0.8571 (t80) cc_final: 0.8361 (t80) REVERT: F 292 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8599 (mttp) REVERT: F 311 ASN cc_start: 0.7639 (t0) cc_final: 0.7284 (t0) REVERT: F 393 ASN cc_start: 0.8582 (m-40) cc_final: 0.8381 (m-40) REVERT: F 443 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8428 (tppt) REVERT: F 444 TYR cc_start: 0.8568 (t80) cc_final: 0.7940 (t80) REVERT: F 448 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8202 (ttmm) REVERT: F 468 THR cc_start: 0.8651 (m) cc_final: 0.8104 (p) REVERT: F 488 LEU cc_start: 0.8319 (tp) cc_final: 0.7874 (tt) REVERT: F 490 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7521 (t0) REVERT: F 492 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: F 499 ARG cc_start: 0.7528 (tpm170) cc_final: 0.6156 (tpt170) REVERT: F 536 LEU cc_start: 0.8810 (mm) cc_final: 0.8379 (tp) REVERT: F 540 GLU cc_start: 0.7448 (pp20) cc_final: 0.7141 (pp20) REVERT: F 563 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8339 (mtpp) REVERT: F 572 THR cc_start: 0.8353 (m) cc_final: 0.8041 (p) REVERT: F 595 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7770 (mm-30) REVERT: F 621 LEU cc_start: 0.7765 (mp) cc_final: 0.7525 (mp) REVERT: F 642 ASN cc_start: 0.8383 (t0) cc_final: 0.8074 (t0) REVERT: F 661 ARG cc_start: 0.7714 (tpt170) cc_final: 0.6703 (tpt170) REVERT: F 676 ASP cc_start: 0.7814 (p0) cc_final: 0.7374 (p0) REVERT: F 687 ASN cc_start: 0.8690 (t0) cc_final: 0.8462 (t0) REVERT: F 696 CYS cc_start: 0.8059 (t) cc_final: 0.7770 (p) REVERT: F 715 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7405 (ttp80) REVERT: F 751 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7196 (tp30) REVERT: F 752 LYS cc_start: 0.8653 (tptp) cc_final: 0.8389 (tptp) REVERT: F 771 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7314 (pp20) outliers start: 108 outliers final: 65 residues processed: 931 average time/residue: 0.4686 time to fit residues: 622.0602 Evaluate side-chains 924 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 847 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 512 LYS Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 183 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN B 426 GLN D 407 GLN D 687 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25782 Z= 0.207 Angle : 0.644 8.939 34986 Z= 0.319 Chirality : 0.043 0.190 4020 Planarity : 0.005 0.085 4488 Dihedral : 12.536 166.184 3816 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.52 % Allowed : 20.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.15), residues: 3240 helix: 0.54 (0.13), residues: 1560 sheet: 0.58 (0.30), residues: 360 loop : -0.46 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 515 HIS 0.009 0.001 HIS E 285 PHE 0.037 0.002 PHE D 587 TYR 0.018 0.001 TYR B 556 ARG 0.013 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 892 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7854 (tp30) cc_final: 0.7374 (tm-30) REVERT: A 301 ASN cc_start: 0.8115 (m-40) cc_final: 0.7689 (t0) REVERT: A 328 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7963 (ttm110) REVERT: A 335 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7647 (mtp-110) REVERT: A 406 ASP cc_start: 0.7380 (t0) cc_final: 0.6896 (m-30) REVERT: A 429 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7616 (mmm-85) REVERT: A 443 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8459 (tppt) REVERT: A 444 TYR cc_start: 0.8441 (t80) cc_final: 0.7992 (t80) REVERT: A 448 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7852 (mttt) REVERT: A 463 GLU cc_start: 0.8064 (tp30) cc_final: 0.7545 (tp30) REVERT: A 485 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7731 (mmtt) REVERT: A 512 LYS cc_start: 0.8427 (tttp) cc_final: 0.8061 (tttm) REVERT: A 523 GLU cc_start: 0.7488 (tp30) cc_final: 0.7000 (tp30) REVERT: A 525 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8371 (ttmt) REVERT: A 540 GLU cc_start: 0.7285 (pp20) cc_final: 0.6979 (pp20) REVERT: A 548 SER cc_start: 0.8647 (m) cc_final: 0.8382 (p) REVERT: A 556 TYR cc_start: 0.8100 (p90) cc_final: 0.7819 (p90) REVERT: A 595 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7714 (mp0) REVERT: A 619 ASP cc_start: 0.7989 (m-30) cc_final: 0.7557 (m-30) REVERT: A 663 ASP cc_start: 0.7575 (p0) cc_final: 0.7084 (p0) REVERT: A 664 GLU cc_start: 0.7765 (pt0) cc_final: 0.7434 (pt0) REVERT: A 695 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8356 (tptp) REVERT: A 717 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 751 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 752 LYS cc_start: 0.8810 (tttm) cc_final: 0.8448 (ttmm) REVERT: A 755 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8272 (ttmt) REVERT: B 301 ASN cc_start: 0.8181 (t0) cc_final: 0.7902 (t0) REVERT: B 311 ASN cc_start: 0.7632 (t0) cc_final: 0.7412 (t0) REVERT: B 328 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7836 (ttm110) REVERT: B 391 ARG cc_start: 0.8087 (ptt-90) cc_final: 0.7286 (ptt-90) REVERT: B 421 ASP cc_start: 0.8084 (t0) cc_final: 0.7793 (t0) REVERT: B 426 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7869 (mm-40) REVERT: B 444 TYR cc_start: 0.8085 (t80) cc_final: 0.7589 (t80) REVERT: B 448 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7882 (ptpt) REVERT: B 486 VAL cc_start: 0.8957 (p) cc_final: 0.8623 (m) REVERT: B 490 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7612 (t0) REVERT: B 512 LYS cc_start: 0.8052 (tttm) cc_final: 0.7779 (tttm) REVERT: B 525 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8120 (mmtp) REVERT: B 534 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8874 (tp) REVERT: B 582 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8478 (mmmm) REVERT: B 585 GLU cc_start: 0.7482 (pt0) cc_final: 0.7013 (pp20) REVERT: B 600 GLU cc_start: 0.7686 (pp20) cc_final: 0.7285 (pp20) REVERT: B 617 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7361 (mp0) REVERT: B 638 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 642 ASN cc_start: 0.8372 (t0) cc_final: 0.7965 (t0) REVERT: B 661 ARG cc_start: 0.7617 (tpt170) cc_final: 0.7200 (tpm170) REVERT: B 689 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8477 (mtm-85) REVERT: B 695 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8257 (tptm) REVERT: B 696 CYS cc_start: 0.8126 (t) cc_final: 0.7821 (t) REVERT: B 715 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7192 (ttt90) REVERT: B 751 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7351 (tp30) REVERT: B 752 LYS cc_start: 0.8761 (tttm) cc_final: 0.8434 (ttmm) REVERT: B 754 PHE cc_start: 0.8335 (t80) cc_final: 0.7912 (t80) REVERT: C 255 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 324 GLU cc_start: 0.7589 (mp0) cc_final: 0.6765 (mp0) REVERT: C 333 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6656 (tm-30) REVERT: C 382 LYS cc_start: 0.7084 (mtmt) cc_final: 0.6804 (mtmm) REVERT: C 393 ASN cc_start: 0.8451 (m-40) cc_final: 0.8217 (m-40) REVERT: C 406 ASP cc_start: 0.7056 (t0) cc_final: 0.6671 (m-30) REVERT: C 410 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6982 (mm-30) REVERT: C 425 LYS cc_start: 0.8671 (mttt) cc_final: 0.8396 (mttt) REVERT: C 426 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8109 (mm-40) REVERT: C 443 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8501 (mmtp) REVERT: C 453 VAL cc_start: 0.8872 (p) cc_final: 0.8484 (m) REVERT: C 484 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8161 (mm) REVERT: C 488 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7453 (tp) REVERT: C 490 ASP cc_start: 0.7905 (t0) cc_final: 0.7277 (t0) REVERT: C 492 GLU cc_start: 0.7771 (mp0) cc_final: 0.7413 (mp0) REVERT: C 512 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7981 (mmmt) REVERT: C 522 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7512 (mm-30) REVERT: C 573 GLU cc_start: 0.7496 (pm20) cc_final: 0.7222 (pm20) REVERT: C 595 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 599 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7679 (ttm-80) REVERT: C 600 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7236 (tm-30) REVERT: C 643 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 661 ARG cc_start: 0.7409 (tpt170) cc_final: 0.6579 (tpt170) REVERT: C 664 GLU cc_start: 0.7890 (tt0) cc_final: 0.7648 (tt0) REVERT: C 696 CYS cc_start: 0.8054 (t) cc_final: 0.7750 (p) REVERT: C 699 LYS cc_start: 0.9074 (tptm) cc_final: 0.8754 (tppp) REVERT: C 715 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7641 (ttp80) REVERT: C 751 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 755 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8292 (tmtt) REVERT: C 771 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7164 (pp20) REVERT: D 252 LYS cc_start: 0.8184 (tppp) cc_final: 0.7850 (tppp) REVERT: D 294 MET cc_start: 0.7821 (ttm) cc_final: 0.7516 (ttp) REVERT: D 301 ASN cc_start: 0.7555 (m110) cc_final: 0.7136 (m110) REVERT: D 328 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8001 (ttm110) REVERT: D 333 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6646 (tm-30) REVERT: D 374 MET cc_start: 0.7941 (tpt) cc_final: 0.7662 (tpp) REVERT: D 426 GLN cc_start: 0.8505 (tp40) cc_final: 0.8062 (tp40) REVERT: D 443 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8312 (mmtp) REVERT: D 444 TYR cc_start: 0.8362 (t80) cc_final: 0.8014 (t80) REVERT: D 522 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 523 GLU cc_start: 0.7511 (tp30) cc_final: 0.6879 (tp30) REVERT: D 527 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8160 (mtpp) REVERT: D 537 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: D 600 GLU cc_start: 0.7593 (pp20) cc_final: 0.7167 (pp20) REVERT: D 604 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8463 (ttmm) REVERT: D 642 ASN cc_start: 0.8273 (t0) cc_final: 0.7859 (t0) REVERT: D 643 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 690 LEU cc_start: 0.9125 (tp) cc_final: 0.8838 (tt) REVERT: D 691 GLU cc_start: 0.8222 (tp30) cc_final: 0.7432 (tp30) REVERT: D 699 LYS cc_start: 0.9181 (tptm) cc_final: 0.8870 (tppp) REVERT: D 751 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7286 (tp30) REVERT: D 755 LYS cc_start: 0.8591 (tttt) cc_final: 0.8268 (tptp) REVERT: E 253 GLU cc_start: 0.7625 (pm20) cc_final: 0.7410 (mp0) REVERT: E 292 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8229 (mttm) REVERT: E 297 ARG cc_start: 0.7357 (tpt90) cc_final: 0.7057 (tpt90) REVERT: E 301 ASN cc_start: 0.8161 (t0) cc_final: 0.7932 (t0) REVERT: E 425 LYS cc_start: 0.8795 (mttm) cc_final: 0.8539 (mmtp) REVERT: E 443 LYS cc_start: 0.8811 (tppt) cc_final: 0.8356 (tppt) REVERT: E 444 TYR cc_start: 0.8341 (t80) cc_final: 0.8017 (t80) REVERT: E 448 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8016 (ttmt) REVERT: E 453 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8771 (m) REVERT: E 488 LEU cc_start: 0.8782 (tt) cc_final: 0.7896 (tp) REVERT: E 490 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7795 (t0) REVERT: E 492 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: E 498 ILE cc_start: 0.7781 (tt) cc_final: 0.7516 (pt) REVERT: E 512 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7754 (ttpt) REVERT: E 585 GLU cc_start: 0.6830 (pt0) cc_final: 0.6612 (pt0) REVERT: E 595 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 600 GLU cc_start: 0.7709 (pp20) cc_final: 0.7200 (pp20) REVERT: E 617 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7446 (mm-30) REVERT: E 642 ASN cc_start: 0.8568 (t0) cc_final: 0.8282 (t0) REVERT: E 661 ARG cc_start: 0.7392 (tpt170) cc_final: 0.6881 (tpt170) REVERT: E 663 ASP cc_start: 0.8261 (p0) cc_final: 0.7837 (p0) REVERT: E 696 CYS cc_start: 0.8063 (t) cc_final: 0.7789 (t) REVERT: E 745 VAL cc_start: 0.8484 (t) cc_final: 0.8081 (m) REVERT: E 751 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7412 (tp30) REVERT: E 752 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8513 (tmtt) REVERT: F 311 ASN cc_start: 0.7617 (t0) cc_final: 0.7276 (t0) REVERT: F 406 ASP cc_start: 0.6259 (t0) cc_final: 0.6018 (m-30) REVERT: F 443 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8292 (mmpt) REVERT: F 444 TYR cc_start: 0.8480 (t80) cc_final: 0.7868 (t80) REVERT: F 468 THR cc_start: 0.8652 (m) cc_final: 0.8103 (p) REVERT: F 485 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7824 (mmtt) REVERT: F 488 LEU cc_start: 0.8245 (tp) cc_final: 0.7754 (tt) REVERT: F 490 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7395 (t0) REVERT: F 492 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: F 499 ARG cc_start: 0.7446 (tpm170) cc_final: 0.6243 (tpt170) REVERT: F 536 LEU cc_start: 0.8785 (mm) cc_final: 0.8347 (tp) REVERT: F 540 GLU cc_start: 0.7427 (pp20) cc_final: 0.7128 (pp20) REVERT: F 572 THR cc_start: 0.8290 (m) cc_final: 0.7906 (p) REVERT: F 573 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7002 (mm-30) REVERT: F 595 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7875 (mm-30) REVERT: F 642 ASN cc_start: 0.8372 (t0) cc_final: 0.8062 (t0) REVERT: F 661 ARG cc_start: 0.7610 (tpt170) cc_final: 0.5976 (tpt90) REVERT: F 663 ASP cc_start: 0.8379 (p0) cc_final: 0.7912 (p0) REVERT: F 687 ASN cc_start: 0.8650 (t0) cc_final: 0.8431 (t0) REVERT: F 694 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8576 (mtpp) REVERT: F 696 CYS cc_start: 0.8038 (t) cc_final: 0.7729 (p) REVERT: F 751 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7134 (tp30) REVERT: F 752 LYS cc_start: 0.8603 (tptp) cc_final: 0.8329 (tptp) REVERT: F 771 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7284 (pp20) outliers start: 122 outliers final: 71 residues processed: 942 average time/residue: 0.4676 time to fit residues: 627.9572 Evaluate side-chains 958 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 873 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 694 LYS Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 512 LYS Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 178 optimal weight: 0.0570 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 0.0470 chunk 263 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 312 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 687 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25782 Z= 0.180 Angle : 0.642 10.711 34986 Z= 0.314 Chirality : 0.042 0.165 4020 Planarity : 0.005 0.094 4488 Dihedral : 12.319 166.885 3816 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.48 % Allowed : 21.41 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.19 (0.15), residues: 3240 helix: 0.54 (0.13), residues: 1560 sheet: 0.61 (0.30), residues: 360 loop : -0.38 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 515 HIS 0.007 0.001 HIS E 285 PHE 0.034 0.002 PHE D 587 TYR 0.030 0.001 TYR D 768 ARG 0.012 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 898 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7788 (tp30) cc_final: 0.7452 (tm-30) REVERT: A 328 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7944 (ttm110) REVERT: A 335 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7583 (mtp-110) REVERT: A 406 ASP cc_start: 0.7344 (t0) cc_final: 0.6894 (m-30) REVERT: A 429 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7579 (mmm-85) REVERT: A 443 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8428 (tppt) REVERT: A 444 TYR cc_start: 0.8393 (t80) cc_final: 0.7954 (t80) REVERT: A 448 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7836 (mttt) REVERT: A 485 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7784 (mmtp) REVERT: A 512 LYS cc_start: 0.8404 (tttp) cc_final: 0.8147 (tttp) REVERT: A 522 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 523 GLU cc_start: 0.7473 (tp30) cc_final: 0.6973 (tp30) REVERT: A 540 GLU cc_start: 0.7254 (pp20) cc_final: 0.6962 (pp20) REVERT: A 548 SER cc_start: 0.8639 (m) cc_final: 0.8424 (p) REVERT: A 556 TYR cc_start: 0.8066 (p90) cc_final: 0.7794 (p90) REVERT: A 595 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7690 (mp0) REVERT: A 638 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8376 (p) REVERT: A 661 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7383 (mmm160) REVERT: A 663 ASP cc_start: 0.7475 (p0) cc_final: 0.6857 (p0) REVERT: A 695 LYS cc_start: 0.8651 (tmtt) cc_final: 0.8350 (tptp) REVERT: A 717 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 751 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 752 LYS cc_start: 0.8818 (tttm) cc_final: 0.8420 (ttmm) REVERT: A 755 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8243 (ttmt) REVERT: B 301 ASN cc_start: 0.8188 (t0) cc_final: 0.7910 (t0) REVERT: B 311 ASN cc_start: 0.7588 (t0) cc_final: 0.7354 (t0) REVERT: B 328 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7816 (ttm110) REVERT: B 391 ARG cc_start: 0.8072 (ptt-90) cc_final: 0.7409 (ptt-90) REVERT: B 426 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8146 (mm-40) REVERT: B 484 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 486 VAL cc_start: 0.8977 (p) cc_final: 0.8661 (m) REVERT: B 490 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7643 (t0) REVERT: B 525 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8088 (mmtp) REVERT: B 534 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8892 (tp) REVERT: B 585 GLU cc_start: 0.7467 (pt0) cc_final: 0.7014 (pp20) REVERT: B 600 GLU cc_start: 0.7662 (pp20) cc_final: 0.7251 (pp20) REVERT: B 617 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7122 (mp0) REVERT: B 638 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 642 ASN cc_start: 0.8328 (t0) cc_final: 0.7893 (t0) REVERT: B 661 ARG cc_start: 0.7626 (tpt170) cc_final: 0.7215 (tpm170) REVERT: B 689 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8476 (mtm-85) REVERT: B 695 LYS cc_start: 0.8520 (tmtt) cc_final: 0.8273 (tptm) REVERT: B 696 CYS cc_start: 0.8047 (t) cc_final: 0.7782 (p) REVERT: B 751 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7342 (tp30) REVERT: B 752 LYS cc_start: 0.8766 (tttm) cc_final: 0.8381 (ttmm) REVERT: C 253 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: C 255 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 348 ASP cc_start: 0.7677 (m-30) cc_final: 0.7440 (m-30) REVERT: C 382 LYS cc_start: 0.7033 (mtmt) cc_final: 0.6755 (mtmm) REVERT: C 406 ASP cc_start: 0.6961 (t0) cc_final: 0.6595 (m-30) REVERT: C 425 LYS cc_start: 0.8598 (mttt) cc_final: 0.8239 (tppp) REVERT: C 443 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8495 (mmtp) REVERT: C 453 VAL cc_start: 0.8885 (p) cc_final: 0.8517 (m) REVERT: C 484 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8113 (mm) REVERT: C 488 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7365 (tp) REVERT: C 490 ASP cc_start: 0.7852 (t0) cc_final: 0.7280 (t0) REVERT: C 492 GLU cc_start: 0.7745 (mp0) cc_final: 0.7353 (mp0) REVERT: C 495 MET cc_start: 0.8323 (ttp) cc_final: 0.8107 (ttm) REVERT: C 512 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7975 (mmmt) REVERT: C 522 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7537 (mm-30) REVERT: C 540 GLU cc_start: 0.7539 (pp20) cc_final: 0.7293 (pp20) REVERT: C 568 LYS cc_start: 0.8322 (mttt) cc_final: 0.8079 (mttt) REVERT: C 585 GLU cc_start: 0.6988 (pt0) cc_final: 0.6651 (pp20) REVERT: C 586 ILE cc_start: 0.8781 (pt) cc_final: 0.7977 (pt) REVERT: C 600 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 643 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 661 ARG cc_start: 0.7308 (tpt170) cc_final: 0.6232 (tpt90) REVERT: C 664 GLU cc_start: 0.7890 (tt0) cc_final: 0.7649 (tt0) REVERT: C 691 GLU cc_start: 0.8123 (tp30) cc_final: 0.7877 (tp30) REVERT: C 710 HIS cc_start: 0.8664 (m90) cc_final: 0.8308 (m-70) REVERT: C 711 GLU cc_start: 0.7729 (pm20) cc_final: 0.7256 (pm20) REVERT: C 715 ARG cc_start: 0.7873 (ttp-170) cc_final: 0.7632 (ttp80) REVERT: C 751 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7438 (tp30) REVERT: C 755 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8267 (tmtt) REVERT: C 771 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7121 (pp20) REVERT: D 252 LYS cc_start: 0.8194 (tppp) cc_final: 0.7803 (tppp) REVERT: D 301 ASN cc_start: 0.7547 (m110) cc_final: 0.7120 (m110) REVERT: D 328 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7989 (ttm110) REVERT: D 333 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6620 (tm-30) REVERT: D 374 MET cc_start: 0.7729 (tpt) cc_final: 0.7438 (tpp) REVERT: D 426 GLN cc_start: 0.8532 (tp40) cc_final: 0.8082 (tp40) REVERT: D 428 SER cc_start: 0.9031 (m) cc_final: 0.8685 (p) REVERT: D 443 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8289 (mmtp) REVERT: D 444 TYR cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: D 492 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 522 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7550 (mm-30) REVERT: D 523 GLU cc_start: 0.7501 (tp30) cc_final: 0.6723 (tp30) REVERT: D 527 LYS cc_start: 0.8693 (mtpp) cc_final: 0.7883 (ttmm) REVERT: D 529 LYS cc_start: 0.8313 (tppp) cc_final: 0.7657 (tppt) REVERT: D 537 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: D 600 GLU cc_start: 0.7589 (pp20) cc_final: 0.7076 (pp20) REVERT: D 604 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8449 (ttmm) REVERT: D 642 ASN cc_start: 0.8277 (t0) cc_final: 0.7854 (t0) REVERT: D 643 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 690 LEU cc_start: 0.9098 (tp) cc_final: 0.8887 (tp) REVERT: D 691 GLU cc_start: 0.8167 (tp30) cc_final: 0.7408 (tp30) REVERT: D 699 LYS cc_start: 0.9166 (tptm) cc_final: 0.8851 (tppp) REVERT: D 712 LEU cc_start: 0.8907 (mp) cc_final: 0.8690 (mt) REVERT: D 751 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7253 (tp30) REVERT: D 755 LYS cc_start: 0.8559 (tttt) cc_final: 0.8231 (tptp) REVERT: D 765 MET cc_start: 0.7911 (mmm) cc_final: 0.7684 (mtt) REVERT: D 769 TYR cc_start: 0.8538 (m-10) cc_final: 0.8312 (m-10) REVERT: E 253 GLU cc_start: 0.7623 (pm20) cc_final: 0.7411 (mp0) REVERT: E 292 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8358 (mtmm) REVERT: E 297 ARG cc_start: 0.7297 (tpt90) cc_final: 0.7015 (tpt90) REVERT: E 301 ASN cc_start: 0.8169 (t0) cc_final: 0.7936 (t0) REVERT: E 390 ASN cc_start: 0.7563 (p0) cc_final: 0.7353 (p0) REVERT: E 443 LYS cc_start: 0.8773 (tppt) cc_final: 0.8296 (tppt) REVERT: E 444 TYR cc_start: 0.8342 (t80) cc_final: 0.8056 (t80) REVERT: E 448 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7976 (ttmt) REVERT: E 453 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (m) REVERT: E 488 LEU cc_start: 0.8691 (tt) cc_final: 0.7698 (tp) REVERT: E 490 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7757 (t0) REVERT: E 492 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: E 498 ILE cc_start: 0.7653 (tt) cc_final: 0.7429 (pt) REVERT: E 512 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7755 (ttpt) REVERT: E 585 GLU cc_start: 0.6833 (pt0) cc_final: 0.6625 (pt0) REVERT: E 600 GLU cc_start: 0.7700 (pp20) cc_final: 0.7194 (pp20) REVERT: E 661 ARG cc_start: 0.7345 (tpt170) cc_final: 0.6798 (tpt170) REVERT: E 663 ASP cc_start: 0.8283 (p0) cc_final: 0.7854 (p0) REVERT: E 696 CYS cc_start: 0.8025 (t) cc_final: 0.7755 (t) REVERT: E 745 VAL cc_start: 0.8464 (t) cc_final: 0.8047 (m) REVERT: E 751 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7366 (tp30) REVERT: E 752 LYS cc_start: 0.8965 (tmtt) cc_final: 0.8481 (tmtt) REVERT: F 258 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8775 (ttmm) REVERT: F 261 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (tp) REVERT: F 292 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8340 (mttp) REVERT: F 311 ASN cc_start: 0.7536 (t0) cc_final: 0.7221 (t0) REVERT: F 406 ASP cc_start: 0.6273 (t0) cc_final: 0.5850 (m-30) REVERT: F 443 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8245 (mmpt) REVERT: F 444 TYR cc_start: 0.8405 (t80) cc_final: 0.7815 (t80) REVERT: F 468 THR cc_start: 0.8629 (m) cc_final: 0.7968 (p) REVERT: F 488 LEU cc_start: 0.8238 (tp) cc_final: 0.7696 (tt) REVERT: F 490 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7423 (t0) REVERT: F 492 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: F 499 ARG cc_start: 0.7351 (tpm170) cc_final: 0.5964 (tpt170) REVERT: F 525 LYS cc_start: 0.8669 (mttm) cc_final: 0.8418 (mmmt) REVERT: F 536 LEU cc_start: 0.8768 (mm) cc_final: 0.8303 (tp) REVERT: F 540 GLU cc_start: 0.7414 (pp20) cc_final: 0.7132 (pp20) REVERT: F 572 THR cc_start: 0.8268 (m) cc_final: 0.7874 (p) REVERT: F 573 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7009 (mm-30) REVERT: F 595 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7739 (mm-30) REVERT: F 642 ASN cc_start: 0.8307 (t0) cc_final: 0.7985 (t0) REVERT: F 661 ARG cc_start: 0.7496 (tpt170) cc_final: 0.5738 (tpt90) REVERT: F 663 ASP cc_start: 0.8346 (p0) cc_final: 0.7830 (p0) REVERT: F 687 ASN cc_start: 0.8614 (t0) cc_final: 0.8409 (t0) REVERT: F 694 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8549 (mtpp) REVERT: F 696 CYS cc_start: 0.8017 (t) cc_final: 0.7714 (p) REVERT: F 715 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7438 (ttp80) REVERT: F 751 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6844 (tm-30) REVERT: F 752 LYS cc_start: 0.8560 (tptp) cc_final: 0.8149 (tptp) REVERT: F 771 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7233 (pp20) outliers start: 121 outliers final: 75 residues processed: 946 average time/residue: 0.4815 time to fit residues: 647.7861 Evaluate side-chains 966 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 871 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 512 LYS Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 737 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 0.0020 chunk 186 optimal weight: 6.9990 chunk 94 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.6430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 HIS ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25782 Z= 0.191 Angle : 0.667 13.565 34986 Z= 0.323 Chirality : 0.043 0.164 4020 Planarity : 0.005 0.079 4488 Dihedral : 12.301 171.922 3816 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.48 % Allowed : 22.37 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.22 (0.15), residues: 3240 helix: 0.57 (0.13), residues: 1560 sheet: 0.53 (0.29), residues: 378 loop : -0.35 (0.19), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 515 HIS 0.006 0.001 HIS E 678 PHE 0.033 0.002 PHE D 587 TYR 0.026 0.001 TYR D 556 ARG 0.013 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 886 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 ASN cc_start: 0.8216 (t0) cc_final: 0.7851 (t0) REVERT: A 324 GLU cc_start: 0.6679 (mp0) cc_final: 0.6185 (mp0) REVERT: A 328 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7942 (ttm110) REVERT: A 333 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 335 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7603 (mtp-110) REVERT: A 406 ASP cc_start: 0.7336 (t0) cc_final: 0.6920 (m-30) REVERT: A 429 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7522 (mmm-85) REVERT: A 444 TYR cc_start: 0.8384 (t80) cc_final: 0.7970 (t80) REVERT: A 448 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7855 (mttt) REVERT: A 485 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7790 (mmtp) REVERT: A 512 LYS cc_start: 0.8360 (tttp) cc_final: 0.8104 (tttp) REVERT: A 522 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 523 GLU cc_start: 0.7478 (tp30) cc_final: 0.6990 (tp30) REVERT: A 537 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: A 540 GLU cc_start: 0.7260 (pp20) cc_final: 0.6960 (pp20) REVERT: A 548 SER cc_start: 0.8628 (m) cc_final: 0.8146 (p) REVERT: A 556 TYR cc_start: 0.8062 (p90) cc_final: 0.7774 (p90) REVERT: A 595 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7731 (mm-30) REVERT: A 638 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 663 ASP cc_start: 0.7439 (p0) cc_final: 0.6822 (p0) REVERT: A 695 LYS cc_start: 0.8661 (tmtt) cc_final: 0.8353 (tptp) REVERT: A 717 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 730 GLU cc_start: 0.7894 (tp30) cc_final: 0.7560 (mm-30) REVERT: A 751 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 752 LYS cc_start: 0.8833 (tttm) cc_final: 0.8410 (ttmm) REVERT: A 755 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8242 (ttmt) REVERT: A 770 GLU cc_start: 0.7694 (mp0) cc_final: 0.7412 (mp0) REVERT: B 301 ASN cc_start: 0.8191 (t0) cc_final: 0.7936 (t0) REVERT: B 311 ASN cc_start: 0.7504 (t0) cc_final: 0.7275 (t0) REVERT: B 328 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7820 (ttm110) REVERT: B 390 ASN cc_start: 0.7494 (p0) cc_final: 0.7292 (p0) REVERT: B 426 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8029 (mm-40) REVERT: B 484 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 486 VAL cc_start: 0.8977 (p) cc_final: 0.8609 (m) REVERT: B 490 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7678 (t0) REVERT: B 497 ASP cc_start: 0.7522 (t0) cc_final: 0.7155 (t0) REVERT: B 499 ARG cc_start: 0.6980 (tpm170) cc_final: 0.6326 (tpm170) REVERT: B 525 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8102 (mmtp) REVERT: B 534 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8875 (tp) REVERT: B 585 GLU cc_start: 0.7472 (pt0) cc_final: 0.6994 (pp20) REVERT: B 600 GLU cc_start: 0.7668 (pp20) cc_final: 0.7243 (pp20) REVERT: B 642 ASN cc_start: 0.8302 (t0) cc_final: 0.7879 (t0) REVERT: B 661 ARG cc_start: 0.7591 (tpt170) cc_final: 0.7254 (tpt170) REVERT: B 676 ASP cc_start: 0.8033 (p0) cc_final: 0.7719 (p0) REVERT: B 695 LYS cc_start: 0.8543 (tmtt) cc_final: 0.8262 (tptm) REVERT: B 696 CYS cc_start: 0.8095 (t) cc_final: 0.7842 (t) REVERT: B 727 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8580 (tp) REVERT: B 751 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7322 (tp30) REVERT: B 752 LYS cc_start: 0.8689 (tttm) cc_final: 0.8313 (ttmm) REVERT: C 253 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: C 255 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7419 (tm-30) REVERT: C 262 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 333 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6647 (tm-30) REVERT: C 406 ASP cc_start: 0.7023 (t0) cc_final: 0.6713 (m-30) REVERT: C 425 LYS cc_start: 0.8567 (mttt) cc_final: 0.8272 (mttt) REVERT: C 426 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8151 (mm-40) REVERT: C 443 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8506 (mmtp) REVERT: C 453 VAL cc_start: 0.8959 (p) cc_final: 0.8633 (m) REVERT: C 484 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mm) REVERT: C 488 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7380 (tp) REVERT: C 490 ASP cc_start: 0.7894 (t0) cc_final: 0.7318 (t0) REVERT: C 492 GLU cc_start: 0.7745 (mp0) cc_final: 0.7330 (mp0) REVERT: C 495 MET cc_start: 0.8309 (ttp) cc_final: 0.8092 (ttm) REVERT: C 512 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7971 (mmmt) REVERT: C 522 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 540 GLU cc_start: 0.7538 (pp20) cc_final: 0.7305 (pp20) REVERT: C 585 GLU cc_start: 0.6978 (pt0) cc_final: 0.6639 (pp20) REVERT: C 586 ILE cc_start: 0.8781 (pt) cc_final: 0.7951 (pt) REVERT: C 600 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 643 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 661 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6614 (tpt170) REVERT: C 664 GLU cc_start: 0.7923 (tt0) cc_final: 0.7702 (tt0) REVERT: C 691 GLU cc_start: 0.8128 (tp30) cc_final: 0.7878 (tp30) REVERT: C 699 LYS cc_start: 0.9030 (tptm) cc_final: 0.8761 (tppp) REVERT: C 711 GLU cc_start: 0.7732 (pm20) cc_final: 0.7257 (pm20) REVERT: C 715 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7654 (ttp80) REVERT: C 751 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7407 (tp30) REVERT: C 755 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8277 (tmtt) REVERT: C 771 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7102 (pp20) REVERT: D 252 LYS cc_start: 0.8210 (tppp) cc_final: 0.7760 (tppp) REVERT: D 301 ASN cc_start: 0.7569 (m110) cc_final: 0.7120 (m110) REVERT: D 328 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7844 (ttm110) REVERT: D 333 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6684 (tm-30) REVERT: D 421 ASP cc_start: 0.8283 (t0) cc_final: 0.7854 (t0) REVERT: D 426 GLN cc_start: 0.8519 (tp40) cc_final: 0.8074 (tp40) REVERT: D 428 SER cc_start: 0.9027 (m) cc_final: 0.8681 (p) REVERT: D 443 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8297 (mmtp) REVERT: D 444 TYR cc_start: 0.8289 (t80) cc_final: 0.7954 (t80) REVERT: D 466 MET cc_start: 0.8601 (tpp) cc_final: 0.8232 (tpp) REVERT: D 523 GLU cc_start: 0.7518 (tp30) cc_final: 0.6875 (tp30) REVERT: D 527 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8150 (mtpp) REVERT: D 537 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: D 600 GLU cc_start: 0.7617 (pp20) cc_final: 0.7108 (pp20) REVERT: D 604 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8445 (ttmm) REVERT: D 642 ASN cc_start: 0.8270 (t0) cc_final: 0.7848 (t0) REVERT: D 643 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7494 (mm-30) REVERT: D 690 LEU cc_start: 0.9113 (tp) cc_final: 0.8840 (tt) REVERT: D 691 GLU cc_start: 0.8167 (tp30) cc_final: 0.7408 (tp30) REVERT: D 699 LYS cc_start: 0.9169 (tptm) cc_final: 0.8861 (tppp) REVERT: D 751 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7260 (tp30) REVERT: D 755 LYS cc_start: 0.8537 (tttt) cc_final: 0.8226 (tptp) REVERT: D 765 MET cc_start: 0.7893 (mmm) cc_final: 0.7681 (mtt) REVERT: E 242 LEU cc_start: 0.8460 (mm) cc_final: 0.8203 (tp) REVERT: E 262 GLU cc_start: 0.7882 (tp30) cc_final: 0.7600 (tm-30) REVERT: E 292 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8171 (mttm) REVERT: E 297 ARG cc_start: 0.7303 (tpt90) cc_final: 0.7021 (tpt90) REVERT: E 301 ASN cc_start: 0.8159 (t0) cc_final: 0.7922 (t0) REVERT: E 443 LYS cc_start: 0.8773 (tppt) cc_final: 0.8295 (tppt) REVERT: E 444 TYR cc_start: 0.8347 (t80) cc_final: 0.8058 (t80) REVERT: E 448 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7968 (ttmt) REVERT: E 453 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8714 (m) REVERT: E 488 LEU cc_start: 0.8653 (tt) cc_final: 0.7625 (tp) REVERT: E 490 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7748 (t0) REVERT: E 492 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: E 498 ILE cc_start: 0.7635 (tt) cc_final: 0.7407 (pt) REVERT: E 600 GLU cc_start: 0.7731 (pp20) cc_final: 0.7205 (pp20) REVERT: E 661 ARG cc_start: 0.7354 (tpt170) cc_final: 0.6597 (tpt90) REVERT: E 696 CYS cc_start: 0.8029 (t) cc_final: 0.7754 (t) REVERT: E 745 VAL cc_start: 0.8430 (t) cc_final: 0.8010 (m) REVERT: E 751 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7359 (tp30) REVERT: E 752 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8491 (tmtt) REVERT: E 755 LYS cc_start: 0.8643 (tttm) cc_final: 0.8337 (ttmm) REVERT: F 292 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8383 (mmtm) REVERT: F 311 ASN cc_start: 0.7523 (t0) cc_final: 0.7211 (t0) REVERT: F 391 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7339 (mtm-85) REVERT: F 406 ASP cc_start: 0.6260 (t0) cc_final: 0.5996 (m-30) REVERT: F 443 LYS cc_start: 0.8680 (mmpt) cc_final: 0.8290 (mmpt) REVERT: F 444 TYR cc_start: 0.8337 (t80) cc_final: 0.7784 (t80) REVERT: F 468 THR cc_start: 0.8646 (m) cc_final: 0.7965 (p) REVERT: F 485 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7693 (mmtt) REVERT: F 488 LEU cc_start: 0.8240 (tp) cc_final: 0.7675 (tt) REVERT: F 490 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7503 (t0) REVERT: F 492 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: F 525 LYS cc_start: 0.8687 (mttm) cc_final: 0.8429 (mmmt) REVERT: F 536 LEU cc_start: 0.8773 (mm) cc_final: 0.8303 (tp) REVERT: F 540 GLU cc_start: 0.7416 (pp20) cc_final: 0.7166 (pp20) REVERT: F 572 THR cc_start: 0.8215 (m) cc_final: 0.7568 (p) REVERT: F 573 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7047 (mm-30) REVERT: F 642 ASN cc_start: 0.8331 (t0) cc_final: 0.7996 (t0) REVERT: F 661 ARG cc_start: 0.7479 (tpt170) cc_final: 0.6424 (tpt170) REVERT: F 691 GLU cc_start: 0.8094 (tp30) cc_final: 0.7500 (tp30) REVERT: F 694 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8597 (mtpp) REVERT: F 715 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7444 (ttp80) REVERT: F 729 GLN cc_start: 0.8433 (mt0) cc_final: 0.8100 (mt0) REVERT: F 751 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6841 (tm-30) REVERT: F 752 LYS cc_start: 0.8560 (tptp) cc_final: 0.8160 (tptp) REVERT: F 770 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7818 (mm-30) outliers start: 121 outliers final: 83 residues processed: 940 average time/residue: 0.4683 time to fit residues: 631.1095 Evaluate side-chains 980 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 879 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 582 LYS Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 737 MET Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 687 ASN F 426 GLN ** F 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 25782 Z= 0.299 Angle : 0.720 10.328 34986 Z= 0.354 Chirality : 0.045 0.219 4020 Planarity : 0.005 0.096 4488 Dihedral : 12.374 172.920 3816 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.26 % Allowed : 23.44 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.21 (0.16), residues: 3240 helix: 0.58 (0.13), residues: 1560 sheet: 0.78 (0.30), residues: 348 loop : -0.44 (0.19), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 515 HIS 0.030 0.001 HIS A 285 PHE 0.034 0.002 PHE D 587 TYR 0.042 0.002 TYR D 768 ARG 0.013 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 882 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7924 (tp30) cc_final: 0.7554 (tm-30) REVERT: A 252 LYS cc_start: 0.8349 (tppp) cc_final: 0.8080 (tppp) REVERT: A 324 GLU cc_start: 0.6825 (mp0) cc_final: 0.6057 (mp0) REVERT: A 328 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7988 (ttm110) REVERT: A 333 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6719 (tm-30) REVERT: A 335 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7656 (mtp-110) REVERT: A 371 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 406 ASP cc_start: 0.7488 (t0) cc_final: 0.6957 (t0) REVERT: A 429 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7591 (mmm-85) REVERT: A 443 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8520 (tppt) REVERT: A 444 TYR cc_start: 0.8435 (t80) cc_final: 0.8103 (t80) REVERT: A 448 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7872 (mttt) REVERT: A 487 THR cc_start: 0.8971 (t) cc_final: 0.8550 (p) REVERT: A 492 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: A 512 LYS cc_start: 0.8395 (tttp) cc_final: 0.8142 (tttp) REVERT: A 523 GLU cc_start: 0.7527 (tp30) cc_final: 0.7064 (tp30) REVERT: A 540 GLU cc_start: 0.7352 (pp20) cc_final: 0.7059 (pp20) REVERT: A 548 SER cc_start: 0.8619 (m) cc_final: 0.8216 (p) REVERT: A 556 TYR cc_start: 0.8194 (p90) cc_final: 0.7985 (p90) REVERT: A 585 GLU cc_start: 0.7471 (pt0) cc_final: 0.7170 (pp20) REVERT: A 595 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7747 (mm-30) REVERT: A 638 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 663 ASP cc_start: 0.7432 (p0) cc_final: 0.6802 (p0) REVERT: A 665 ILE cc_start: 0.8497 (mm) cc_final: 0.8272 (tt) REVERT: A 695 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8389 (tptp) REVERT: A 704 GLU cc_start: 0.7198 (pm20) cc_final: 0.6889 (pm20) REVERT: A 751 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7042 (tp30) REVERT: A 752 LYS cc_start: 0.8842 (tttm) cc_final: 0.8552 (ttmm) REVERT: A 755 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8265 (ttmt) REVERT: B 301 ASN cc_start: 0.8228 (t0) cc_final: 0.7979 (t0) REVERT: B 311 ASN cc_start: 0.7557 (t0) cc_final: 0.7318 (t0) REVERT: B 328 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7857 (ttm110) REVERT: B 406 ASP cc_start: 0.7471 (t0) cc_final: 0.7237 (t0) REVERT: B 422 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8867 (mt) REVERT: B 426 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8188 (mm-40) REVERT: B 443 LYS cc_start: 0.8807 (tppt) cc_final: 0.8432 (mppt) REVERT: B 484 LEU cc_start: 0.8508 (mm) cc_final: 0.8297 (mm) REVERT: B 490 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7693 (t0) REVERT: B 497 ASP cc_start: 0.7597 (t0) cc_final: 0.7198 (t0) REVERT: B 499 ARG cc_start: 0.7204 (tpm170) cc_final: 0.6833 (tpm170) REVERT: B 512 LYS cc_start: 0.7919 (tttm) cc_final: 0.7666 (tttp) REVERT: B 525 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8094 (mmtp) REVERT: B 534 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 572 THR cc_start: 0.8064 (m) cc_final: 0.7715 (p) REVERT: B 585 GLU cc_start: 0.7550 (pt0) cc_final: 0.7048 (pp20) REVERT: B 587 PHE cc_start: 0.7405 (t80) cc_final: 0.7190 (t80) REVERT: B 600 GLU cc_start: 0.7746 (pp20) cc_final: 0.7336 (pp20) REVERT: B 642 ASN cc_start: 0.8317 (t0) cc_final: 0.7897 (t0) REVERT: B 661 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7071 (tpt170) REVERT: B 695 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8314 (tptm) REVERT: B 696 CYS cc_start: 0.8147 (t) cc_final: 0.7851 (p) REVERT: B 751 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7415 (tp30) REVERT: B 752 LYS cc_start: 0.8727 (tttm) cc_final: 0.8330 (ttmm) REVERT: C 253 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: C 255 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 297 ARG cc_start: 0.7272 (tpt170) cc_final: 0.6869 (tpt170) REVERT: C 333 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6726 (tm-30) REVERT: C 406 ASP cc_start: 0.7112 (t0) cc_final: 0.6453 (m-30) REVERT: C 425 LYS cc_start: 0.8629 (mttt) cc_final: 0.8267 (tppp) REVERT: C 443 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8535 (mmtp) REVERT: C 453 VAL cc_start: 0.9017 (p) cc_final: 0.8699 (m) REVERT: C 484 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 488 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7407 (tp) REVERT: C 490 ASP cc_start: 0.7956 (t0) cc_final: 0.7396 (t0) REVERT: C 492 GLU cc_start: 0.7810 (mp0) cc_final: 0.7362 (mp0) REVERT: C 495 MET cc_start: 0.8339 (ttp) cc_final: 0.8125 (ttm) REVERT: C 512 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8043 (mmmt) REVERT: C 522 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7582 (mm-30) REVERT: C 540 GLU cc_start: 0.7603 (pp20) cc_final: 0.7367 (pp20) REVERT: C 585 GLU cc_start: 0.7049 (pt0) cc_final: 0.6651 (pp20) REVERT: C 586 ILE cc_start: 0.8833 (pt) cc_final: 0.7865 (pt) REVERT: C 600 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 643 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 661 ARG cc_start: 0.7425 (tpt170) cc_final: 0.6371 (tpt90) REVERT: C 664 GLU cc_start: 0.7949 (tt0) cc_final: 0.7744 (tt0) REVERT: C 691 GLU cc_start: 0.8114 (tp30) cc_final: 0.7707 (tp30) REVERT: C 699 LYS cc_start: 0.9100 (tptm) cc_final: 0.8877 (tppt) REVERT: C 710 HIS cc_start: 0.8659 (m90) cc_final: 0.8305 (m-70) REVERT: C 711 GLU cc_start: 0.7804 (pm20) cc_final: 0.7211 (pm20) REVERT: C 715 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7622 (ttp80) REVERT: C 751 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7476 (tp30) REVERT: C 755 LYS cc_start: 0.8571 (tmtt) cc_final: 0.8348 (tmtt) REVERT: C 771 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: D 252 LYS cc_start: 0.8207 (tppp) cc_final: 0.7784 (tppp) REVERT: D 301 ASN cc_start: 0.7614 (m110) cc_final: 0.7182 (m110) REVERT: D 328 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7881 (ttm110) REVERT: D 333 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6758 (tm-30) REVERT: D 426 GLN cc_start: 0.8589 (tp40) cc_final: 0.8164 (tp40) REVERT: D 428 SER cc_start: 0.9135 (m) cc_final: 0.8806 (p) REVERT: D 443 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8358 (mmtp) REVERT: D 444 TYR cc_start: 0.8364 (t80) cc_final: 0.7995 (t80) REVERT: D 467 LYS cc_start: 0.8605 (mttm) cc_final: 0.8398 (mmtp) REVERT: D 523 GLU cc_start: 0.7575 (tp30) cc_final: 0.6952 (tp30) REVERT: D 527 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8193 (mtpp) REVERT: D 537 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6461 (mp0) REVERT: D 600 GLU cc_start: 0.7691 (pp20) cc_final: 0.7147 (pp20) REVERT: D 642 ASN cc_start: 0.8289 (t0) cc_final: 0.7872 (t0) REVERT: D 643 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 690 LEU cc_start: 0.9113 (tp) cc_final: 0.8861 (tt) REVERT: D 691 GLU cc_start: 0.8208 (tp30) cc_final: 0.7473 (tp30) REVERT: D 699 LYS cc_start: 0.9178 (tptm) cc_final: 0.8868 (tppp) REVERT: D 751 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7314 (tp30) REVERT: D 752 LYS cc_start: 0.8792 (tptp) cc_final: 0.8436 (tptp) REVERT: D 755 LYS cc_start: 0.8578 (tttt) cc_final: 0.8271 (tptp) REVERT: E 292 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8216 (mttm) REVERT: E 297 ARG cc_start: 0.7405 (tpt90) cc_final: 0.7132 (tpt90) REVERT: E 301 ASN cc_start: 0.8213 (t0) cc_final: 0.7970 (t0) REVERT: E 382 LYS cc_start: 0.7053 (mtpt) cc_final: 0.6755 (mtpt) REVERT: E 391 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7447 (ptt-90) REVERT: E 443 LYS cc_start: 0.8847 (tppt) cc_final: 0.8393 (tppt) REVERT: E 444 TYR cc_start: 0.8378 (t80) cc_final: 0.8055 (t80) REVERT: E 448 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8027 (ttmt) REVERT: E 488 LEU cc_start: 0.8692 (tt) cc_final: 0.7677 (tp) REVERT: E 490 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7781 (t0) REVERT: E 492 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: E 498 ILE cc_start: 0.7829 (tt) cc_final: 0.7532 (pt) REVERT: E 512 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7863 (ttpt) REVERT: E 595 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 600 GLU cc_start: 0.7800 (pp20) cc_final: 0.7306 (pp20) REVERT: E 661 ARG cc_start: 0.7577 (tpt170) cc_final: 0.6818 (tpt170) REVERT: E 663 ASP cc_start: 0.8427 (p0) cc_final: 0.8009 (p0) REVERT: E 745 VAL cc_start: 0.8507 (t) cc_final: 0.8097 (m) REVERT: E 751 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7407 (tp30) REVERT: E 752 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8485 (tmtt) REVERT: E 755 LYS cc_start: 0.8697 (tttm) cc_final: 0.8391 (ttmm) REVERT: F 261 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8861 (tp) REVERT: F 262 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7735 (tm-30) REVERT: F 292 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8492 (mttp) REVERT: F 311 ASN cc_start: 0.7581 (t0) cc_final: 0.7256 (t0) REVERT: F 391 ARG cc_start: 0.7690 (mtm180) cc_final: 0.7367 (mtm-85) REVERT: F 406 ASP cc_start: 0.6569 (t0) cc_final: 0.6063 (m-30) REVERT: F 443 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8471 (mmtt) REVERT: F 444 TYR cc_start: 0.8429 (t80) cc_final: 0.7769 (t80) REVERT: F 448 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8211 (ttmm) REVERT: F 463 GLU cc_start: 0.8038 (tp30) cc_final: 0.7721 (tp30) REVERT: F 468 THR cc_start: 0.8647 (m) cc_final: 0.7999 (p) REVERT: F 488 LEU cc_start: 0.8277 (tp) cc_final: 0.7676 (tt) REVERT: F 490 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7567 (t0) REVERT: F 492 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: F 499 ARG cc_start: 0.7517 (tpm170) cc_final: 0.6323 (tpt170) REVERT: F 536 LEU cc_start: 0.8813 (mm) cc_final: 0.8466 (tp) REVERT: F 540 GLU cc_start: 0.7491 (pp20) cc_final: 0.7265 (pp20) REVERT: F 642 ASN cc_start: 0.8394 (t0) cc_final: 0.8061 (t0) REVERT: F 661 ARG cc_start: 0.7582 (tpt170) cc_final: 0.6687 (tpt90) REVERT: F 691 GLU cc_start: 0.8132 (tp30) cc_final: 0.7521 (tp30) REVERT: F 694 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8636 (mtpp) REVERT: F 715 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7514 (ttp80) REVERT: F 729 GLN cc_start: 0.8469 (mt0) cc_final: 0.8149 (mt0) REVERT: F 751 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6907 (tm-30) REVERT: F 752 LYS cc_start: 0.8594 (tptp) cc_final: 0.8262 (tptp) REVERT: F 770 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7858 (mm-30) outliers start: 115 outliers final: 75 residues processed: 937 average time/residue: 0.4772 time to fit residues: 638.2091 Evaluate side-chains 963 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 869 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 582 LYS Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 322 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 HIS D 687 ASN F 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25782 Z= 0.214 Angle : 0.716 21.413 34986 Z= 0.347 Chirality : 0.043 0.266 4020 Planarity : 0.005 0.094 4488 Dihedral : 12.276 172.119 3816 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.78 % Allowed : 24.22 % Favored : 72.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.16), residues: 3240 helix: 0.64 (0.13), residues: 1542 sheet: 0.72 (0.30), residues: 348 loop : -0.41 (0.19), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 515 HIS 0.007 0.001 HIS E 678 PHE 0.032 0.002 PHE D 587 TYR 0.022 0.001 TYR D 556 ARG 0.014 0.001 ARG B 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 870 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8287 (tppp) cc_final: 0.7976 (tppp) REVERT: A 324 GLU cc_start: 0.6773 (mp0) cc_final: 0.6233 (mp0) REVERT: A 328 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7963 (ttm110) REVERT: A 333 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 335 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7605 (mtp-110) REVERT: A 371 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7915 (mm) REVERT: A 410 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6691 (mm-30) REVERT: A 429 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7568 (mmm-85) REVERT: A 443 LYS cc_start: 0.8840 (mmpt) cc_final: 0.8462 (tppt) REVERT: A 444 TYR cc_start: 0.8398 (t80) cc_final: 0.8125 (t80) REVERT: A 448 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7868 (mttt) REVERT: A 485 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7533 (mmmt) REVERT: A 487 THR cc_start: 0.8950 (t) cc_final: 0.8535 (p) REVERT: A 492 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: A 512 LYS cc_start: 0.8323 (tttp) cc_final: 0.8082 (tttp) REVERT: A 523 GLU cc_start: 0.7503 (tp30) cc_final: 0.7029 (tp30) REVERT: A 537 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6618 (pm20) REVERT: A 540 GLU cc_start: 0.7302 (pp20) cc_final: 0.7003 (pp20) REVERT: A 548 SER cc_start: 0.8610 (m) cc_final: 0.8164 (p) REVERT: A 556 TYR cc_start: 0.8065 (p90) cc_final: 0.7855 (p90) REVERT: A 585 GLU cc_start: 0.7455 (pt0) cc_final: 0.7154 (pp20) REVERT: A 595 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7605 (mp0) REVERT: A 638 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 660 ASN cc_start: 0.8467 (p0) cc_final: 0.7962 (p0) REVERT: A 663 ASP cc_start: 0.7445 (p0) cc_final: 0.6820 (p0) REVERT: A 665 ILE cc_start: 0.8438 (mm) cc_final: 0.8223 (tt) REVERT: A 695 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8350 (tptp) REVERT: A 717 GLU cc_start: 0.7663 (tp30) cc_final: 0.7453 (tp30) REVERT: A 751 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6998 (tp30) REVERT: A 752 LYS cc_start: 0.8852 (tttm) cc_final: 0.8574 (ttmm) REVERT: A 755 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8222 (ttmt) REVERT: B 301 ASN cc_start: 0.8225 (t0) cc_final: 0.7950 (t0) REVERT: B 311 ASN cc_start: 0.7524 (t0) cc_final: 0.7291 (t0) REVERT: B 328 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7813 (ttm110) REVERT: B 391 ARG cc_start: 0.7871 (ptt-90) cc_final: 0.7076 (ptt-90) REVERT: B 406 ASP cc_start: 0.7477 (t0) cc_final: 0.7244 (t0) REVERT: B 426 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 443 LYS cc_start: 0.8809 (tppt) cc_final: 0.8457 (mppt) REVERT: B 490 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 497 ASP cc_start: 0.7564 (t0) cc_final: 0.7206 (t0) REVERT: B 499 ARG cc_start: 0.7025 (tpm170) cc_final: 0.6726 (tpm170) REVERT: B 512 LYS cc_start: 0.7955 (tttm) cc_final: 0.7678 (tttp) REVERT: B 525 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: B 534 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8848 (tp) REVERT: B 572 THR cc_start: 0.7981 (m) cc_final: 0.7689 (p) REVERT: B 585 GLU cc_start: 0.7504 (pt0) cc_final: 0.6991 (pp20) REVERT: B 600 GLU cc_start: 0.7690 (pp20) cc_final: 0.7272 (pp20) REVERT: B 642 ASN cc_start: 0.8279 (t0) cc_final: 0.7846 (t0) REVERT: B 661 ARG cc_start: 0.7642 (tpt170) cc_final: 0.7295 (tpt170) REVERT: B 676 ASP cc_start: 0.8078 (p0) cc_final: 0.7400 (p0) REVERT: B 695 LYS cc_start: 0.8539 (tmtt) cc_final: 0.8295 (tptm) REVERT: B 696 CYS cc_start: 0.8101 (t) cc_final: 0.7811 (p) REVERT: B 727 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8654 (tp) REVERT: B 751 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7356 (tp30) REVERT: B 752 LYS cc_start: 0.8694 (tttm) cc_final: 0.8295 (ttmm) REVERT: C 253 GLU cc_start: 0.7553 (pt0) cc_final: 0.7176 (pt0) REVERT: C 255 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 258 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8806 (ttmm) REVERT: C 283 LEU cc_start: 0.8444 (tt) cc_final: 0.8230 (tt) REVERT: C 297 ARG cc_start: 0.7214 (tpt170) cc_final: 0.6860 (tpt170) REVERT: C 333 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6689 (tm-30) REVERT: C 391 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7462 (mtm-85) REVERT: C 406 ASP cc_start: 0.6900 (t0) cc_final: 0.6695 (m-30) REVERT: C 425 LYS cc_start: 0.8580 (mttt) cc_final: 0.8172 (tppp) REVERT: C 443 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8523 (mmtp) REVERT: C 453 VAL cc_start: 0.8992 (p) cc_final: 0.8659 (m) REVERT: C 484 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (mm) REVERT: C 488 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7339 (tp) REVERT: C 490 ASP cc_start: 0.7896 (t0) cc_final: 0.7427 (t0) REVERT: C 492 GLU cc_start: 0.7715 (mp0) cc_final: 0.7278 (mp0) REVERT: C 512 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8043 (mmmt) REVERT: C 522 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7542 (mm-30) REVERT: C 540 GLU cc_start: 0.7534 (pp20) cc_final: 0.7325 (pp20) REVERT: C 585 GLU cc_start: 0.6965 (pt0) cc_final: 0.6576 (pp20) REVERT: C 586 ILE cc_start: 0.8819 (pt) cc_final: 0.7870 (pt) REVERT: C 600 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 643 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7753 (mm-30) REVERT: C 661 ARG cc_start: 0.7329 (tpt170) cc_final: 0.6681 (tpt170) REVERT: C 664 GLU cc_start: 0.7932 (tt0) cc_final: 0.7724 (tt0) REVERT: C 691 GLU cc_start: 0.8018 (tp30) cc_final: 0.7634 (tp30) REVERT: C 699 LYS cc_start: 0.9075 (tptm) cc_final: 0.8839 (tppt) REVERT: C 711 GLU cc_start: 0.7781 (pm20) cc_final: 0.7157 (pm20) REVERT: C 715 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7606 (ttp80) REVERT: C 751 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7455 (tp30) REVERT: C 755 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8303 (tmtt) REVERT: C 771 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: D 252 LYS cc_start: 0.8152 (tppp) cc_final: 0.7739 (tppp) REVERT: D 301 ASN cc_start: 0.7598 (m110) cc_final: 0.7148 (m110) REVERT: D 328 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7814 (ttm110) REVERT: D 333 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6701 (tm-30) REVERT: D 426 GLN cc_start: 0.8595 (tp40) cc_final: 0.8131 (tp40) REVERT: D 428 SER cc_start: 0.9116 (m) cc_final: 0.8767 (p) REVERT: D 443 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8369 (mmtp) REVERT: D 444 TYR cc_start: 0.8350 (t80) cc_final: 0.7975 (t80) REVERT: D 466 MET cc_start: 0.8654 (tpp) cc_final: 0.8239 (tpp) REVERT: D 467 LYS cc_start: 0.8566 (mttm) cc_final: 0.8343 (mmtp) REVERT: D 523 GLU cc_start: 0.7535 (tp30) cc_final: 0.6909 (tp30) REVERT: D 527 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8160 (mtpp) REVERT: D 537 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: D 600 GLU cc_start: 0.7637 (pp20) cc_final: 0.7128 (pp20) REVERT: D 642 ASN cc_start: 0.8281 (t0) cc_final: 0.7872 (t0) REVERT: D 643 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 690 LEU cc_start: 0.9091 (tp) cc_final: 0.8859 (tt) REVERT: D 691 GLU cc_start: 0.8167 (tp30) cc_final: 0.7399 (tp30) REVERT: D 699 LYS cc_start: 0.9165 (tptm) cc_final: 0.8854 (tppp) REVERT: D 751 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7268 (tp30) REVERT: D 755 LYS cc_start: 0.8525 (tttt) cc_final: 0.8226 (tptp) REVERT: E 242 LEU cc_start: 0.8431 (mm) cc_final: 0.8186 (tp) REVERT: E 292 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8328 (mtmm) REVERT: E 297 ARG cc_start: 0.7319 (tpt90) cc_final: 0.7042 (tpt90) REVERT: E 301 ASN cc_start: 0.8163 (t0) cc_final: 0.7914 (t0) REVERT: E 382 LYS cc_start: 0.6986 (mtpt) cc_final: 0.6690 (mtpt) REVERT: E 391 ARG cc_start: 0.7790 (ptt-90) cc_final: 0.7341 (ptt-90) REVERT: E 443 LYS cc_start: 0.8815 (tppt) cc_final: 0.8342 (tppt) REVERT: E 444 TYR cc_start: 0.8295 (t80) cc_final: 0.7994 (t80) REVERT: E 448 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8018 (ttmt) REVERT: E 488 LEU cc_start: 0.8648 (tt) cc_final: 0.7550 (tp) REVERT: E 490 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7800 (t0) REVERT: E 492 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: E 498 ILE cc_start: 0.7743 (tt) cc_final: 0.7457 (pt) REVERT: E 595 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7583 (mm-30) REVERT: E 600 GLU cc_start: 0.7734 (pp20) cc_final: 0.7231 (pp20) REVERT: E 661 ARG cc_start: 0.7480 (tpt170) cc_final: 0.6619 (tpt90) REVERT: E 663 ASP cc_start: 0.8414 (p0) cc_final: 0.7961 (p0) REVERT: E 696 CYS cc_start: 0.8039 (t) cc_final: 0.7767 (t) REVERT: E 745 VAL cc_start: 0.8471 (t) cc_final: 0.8056 (m) REVERT: E 751 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7323 (tp30) REVERT: E 752 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8477 (tmtt) REVERT: E 755 LYS cc_start: 0.8645 (tttm) cc_final: 0.8325 (ttmm) REVERT: F 261 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8844 (tp) REVERT: F 311 ASN cc_start: 0.7528 (t0) cc_final: 0.7209 (t0) REVERT: F 391 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7321 (mtm-85) REVERT: F 401 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7690 (mmp80) REVERT: F 406 ASP cc_start: 0.6560 (t0) cc_final: 0.6150 (m-30) REVERT: F 443 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (mmtt) REVERT: F 444 TYR cc_start: 0.8347 (t80) cc_final: 0.7786 (t80) REVERT: F 468 THR cc_start: 0.8652 (m) cc_final: 0.7990 (p) REVERT: F 488 LEU cc_start: 0.8248 (tp) cc_final: 0.7644 (tt) REVERT: F 490 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7519 (t0) REVERT: F 492 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: F 525 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8382 (mmmt) REVERT: F 536 LEU cc_start: 0.8797 (mm) cc_final: 0.8440 (tp) REVERT: F 540 GLU cc_start: 0.7462 (pp20) cc_final: 0.7223 (pp20) REVERT: F 572 THR cc_start: 0.8121 (m) cc_final: 0.7652 (p) REVERT: F 642 ASN cc_start: 0.8379 (t0) cc_final: 0.8041 (t0) REVERT: F 661 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6099 (tpt90) REVERT: F 691 GLU cc_start: 0.8102 (tp30) cc_final: 0.7482 (tp30) REVERT: F 694 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8609 (mtpp) REVERT: F 715 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7460 (ttp80) REVERT: F 729 GLN cc_start: 0.8468 (mt0) cc_final: 0.8109 (mt0) REVERT: F 751 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6858 (tm-30) REVERT: F 752 LYS cc_start: 0.8555 (tptp) cc_final: 0.8197 (tptp) REVERT: F 770 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7852 (mm-30) outliers start: 102 outliers final: 75 residues processed: 914 average time/residue: 0.5002 time to fit residues: 657.3767 Evaluate side-chains 971 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 878 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 619 ASP Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 582 LYS Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 619 ASP Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 737 MET Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 237 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 257 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 264 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117675 restraints weight = 43920.724| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.47 r_work: 0.3365 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25782 Z= 0.195 Angle : 0.700 13.227 34986 Z= 0.338 Chirality : 0.043 0.192 4020 Planarity : 0.005 0.082 4488 Dihedral : 12.053 170.566 3816 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.59 % Allowed : 24.19 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.24 (0.15), residues: 3240 helix: 0.61 (0.13), residues: 1548 sheet: 0.59 (0.30), residues: 366 loop : -0.37 (0.19), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 515 HIS 0.007 0.001 HIS E 678 PHE 0.032 0.002 PHE E 754 TYR 0.022 0.001 TYR D 556 ARG 0.013 0.001 ARG F 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9515.08 seconds wall clock time: 169 minutes 37.91 seconds (10177.91 seconds total)