Starting phenix.real_space_refine on Thu Feb 22 03:58:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn4_4942/02_2024/6rn4_4942_updated.pdb" } resolution = 4.2 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 126 5.16 5 C 20458 2.51 5 N 5926 2.21 5 O 6291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32833 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5364 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: "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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.47, per 1000 atoms: 0.50 Number of scatterers: 32833 At special positions: 0 Unit cell: (141.44, 183.04, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 32 15.00 O 6291 8.00 N 5926 7.00 C 20458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.93 Conformation dependent library (CDL) restraints added in 5.6 seconds 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 26 sheets defined 56.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 243 through 248 removed outlier: 5.162A pdb=" N GLY A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 296 through 304 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 4.454A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 410 through 429 Processing helix chain 'A' and resid 444 through 492 Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.791A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 661 through 667 removed outlier: 3.985A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 815 through 834 Proline residue: A 828 - end of helix Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.737A pdb=" N TYR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.557A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 301 through 304 No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 388 through 405 Processing helix chain 'B' and resid 410 through 429 Processing helix chain 'B' and resid 444 through 492 Processing helix chain 'B' and resid 495 through 523 removed outlier: 4.168A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 611 through 623 Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.678A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 815 through 833 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.607A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 254 through 269 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 297 through 304 Proline residue: C 301 - end of helix Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.897A pdb=" N ARG C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.655A pdb=" N ARG C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 444 through 492 Processing helix chain 'C' and resid 495 through 523 removed outlier: 4.096A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 642 through 646 Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 751 through 754 No H-bonds generated for 'chain 'C' and resid 751 through 754' Processing helix chain 'C' and resid 768 through 789 removed outlier: 3.761A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 807 removed outlier: 3.783A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 299 through 305 removed outlier: 4.351A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG D 305 " --> pdb=" O PRO D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.593A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 429 Processing helix chain 'D' and resid 444 through 492 Processing helix chain 'D' and resid 495 through 523 removed outlier: 4.155A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 553 through 560 Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.716A pdb=" N HIS D 567 " --> pdb=" O GLU D 563 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 588 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 643 through 646 No H-bonds generated for 'chain 'D' and resid 643 through 646' Processing helix chain 'D' and resid 654 through 656 No H-bonds generated for 'chain 'D' and resid 654 through 656' Processing helix chain 'D' and resid 662 through 667 Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 735 through 748 Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 815 through 834 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 247 removed outlier: 3.668A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 296 through 305 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 327 through 332 removed outlier: 5.574A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 332 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 361 removed outlier: 4.928A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 444 through 492 Processing helix chain 'E' and resid 496 through 523 Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 533 through 544 Processing helix chain 'E' and resid 553 through 569 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 611 through 623 Processing helix chain 'E' and resid 640 through 646 removed outlier: 3.508A pdb=" N VAL E 643 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 662 through 667 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 686 through 695 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 735 through 748 Processing helix chain 'E' and resid 751 through 754 No H-bonds generated for 'chain 'E' and resid 751 through 754' Processing helix chain 'E' and resid 768 through 789 removed outlier: 3.950A pdb=" N GLU E 788 " --> pdb=" O LYS E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 806 removed outlier: 3.902A pdb=" N LYS E 801 " --> pdb=" O ASP E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 161 through 164 No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 224 Processing helix chain 'F' and resid 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 296 through 305 Proline residue: F 301 - end of helix removed outlier: 3.680A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 322 removed outlier: 3.937A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.907A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 411 through 429 Processing helix chain 'F' and resid 444 through 492 Processing helix chain 'F' and resid 495 through 523 removed outlier: 4.232A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 555 through 567 removed outlier: 4.308A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 589 Processing helix chain 'F' and resid 611 through 621 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 642 through 647 Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 684 through 695 removed outlier: 3.570A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 728 Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 769 through 789 Processing helix chain 'F' and resid 797 through 807 Processing helix chain 'F' and resid 814 through 833 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.212A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 236 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 599 through 603 removed outlier: 6.992A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 793 through 795 removed outlier: 5.973A pdb=" N ILE A 844 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 Processing sheet with id= F, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.432A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 760 through 763 removed outlier: 8.339A pdb=" N VAL B 761 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 602 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE B 763 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU B 604 " --> pdb=" O PHE B 763 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= I, first strand: chain 'B' and resid 792 through 795 removed outlier: 3.694A pdb=" N ARG B 845 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 165 through 167 Processing sheet with id= K, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.146A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 600 through 603 removed outlier: 7.335A pdb=" N VAL C 714 " --> pdb=" O PHE C 601 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N PHE C 603 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET C 716 " --> pdb=" O PHE C 603 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 793 through 795 removed outlier: 5.923A pdb=" N ILE C 844 " --> pdb=" O HIS C 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 165 through 167 Processing sheet with id= O, first strand: chain 'D' and resid 202 through 205 removed outlier: 6.160A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 715 through 717 removed outlier: 6.652A pdb=" N PHE D 601 " --> pdb=" O MET D 716 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU D 759 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU D 604 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL D 761 " --> pdb=" O LEU D 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 631 through 633 removed outlier: 5.347A pdb=" N LEU D 675 " --> pdb=" O ILE D 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.501A pdb=" N HIS D 794 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 165 through 167 Processing sheet with id= T, first strand: chain 'E' and resid 311 through 315 removed outlier: 8.125A pdb=" N THR E 314 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 760 through 762 removed outlier: 8.193A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 846 through 848 Processing sheet with id= W, first strand: chain 'F' and resid 165 through 167 Processing sheet with id= X, first strand: chain 'F' and resid 333 through 337 removed outlier: 7.209A pdb=" N ASN F 201 " --> pdb=" O GLN F 334 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 336 " --> pdb=" O ASN F 201 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL F 203 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 759 through 763 removed outlier: 3.678A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 718 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 605 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 675 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 632 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 677 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 793 through 795 removed outlier: 5.822A pdb=" N ILE F 844 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 843 " --> pdb=" O HIS F 858 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 858 " --> pdb=" O VAL F 843 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1577 hydrogen bonds defined for protein. 4698 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: 13.08 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 5973 1.32 - 1.48: 12611 1.48 - 1.64: 14471 1.64 - 1.80: 183 1.80 - 1.96: 47 Bond restraints: 33285 Sorted by residual: bond pdb=" C GLY B 253 " pdb=" N GLU B 254 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.46e-02 4.69e+03 1.60e+01 bond pdb=" C LEU D 177 " pdb=" N ASP D 178 " ideal model delta sigma weight residual 1.331 1.271 0.061 1.63e-02 3.76e+03 1.39e+01 bond pdb=" CB GLU E 613 " pdb=" CG GLU E 613 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.33e+01 bond pdb=" CB ASP D 388 " pdb=" CG ASP D 388 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.20e+01 ... (remaining 33280 not shown) Histogram of bond angle deviations from ideal: 74.10 - 88.91: 1 88.91 - 103.71: 465 103.71 - 118.52: 26599 118.52 - 133.32: 17849 133.32 - 148.13: 15 Bond angle restraints: 44929 Sorted by residual: angle pdb=" O1B AGS F1001 " pdb=" PB AGS F1001 " pdb=" O2B AGS F1001 " ideal model delta sigma weight residual 112.09 74.10 37.99 4.09e+00 5.99e-02 8.64e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CA PRO F 409 " ideal model delta sigma weight residual 127.00 148.13 -21.13 2.40e+00 1.74e-01 7.75e+01 angle pdb=" N VAL C 686 " pdb=" CA VAL C 686 " pdb=" C VAL C 686 " ideal model delta sigma weight residual 113.22 103.26 9.96 1.23e+00 6.61e-01 6.56e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CD PRO F 409 " ideal model delta sigma weight residual 120.60 103.04 17.56 2.20e+00 2.07e-01 6.37e+01 angle pdb=" N LEU F 444 " pdb=" CA LEU F 444 " pdb=" C LEU F 444 " ideal model delta sigma weight residual 113.50 106.14 7.36 1.23e+00 6.61e-01 3.58e+01 ... (remaining 44924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.66: 20139 27.66 - 55.31: 463 55.31 - 82.97: 36 82.97 - 110.62: 0 110.62 - 138.28: 2 Dihedral angle restraints: 20640 sinusoidal: 8765 harmonic: 11875 Sorted by residual: dihedral pdb=" CA GLY F 608 " pdb=" C GLY F 608 " pdb=" N VAL F 609 " pdb=" CA VAL F 609 " ideal model delta harmonic sigma weight residual -180.00 -131.68 -48.32 0 5.00e+00 4.00e-02 9.34e+01 dihedral pdb=" CA TYR A 656 " pdb=" C TYR A 656 " pdb=" N GLU A 657 " pdb=" CA GLU A 657 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA VAL B 548 " pdb=" C VAL B 548 " pdb=" N SER B 549 " pdb=" CA SER B 549 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 20637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4288 0.085 - 0.171: 749 0.171 - 0.256: 45 0.256 - 0.342: 5 0.342 - 0.427: 1 Chirality restraints: 5088 Sorted by residual: chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.75 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" PA AGS C1001 " pdb=" O2A AGS C1001 " pdb=" O3A AGS C1001 " pdb=" O5' AGS C1001 " both_signs ideal model delta sigma weight residual True 3.18 -2.89 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5085 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 661 " -0.036 2.00e-02 2.50e+03 2.79e-02 1.56e+01 pdb=" CG TYR E 661 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR E 661 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 661 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 661 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 661 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 661 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 661 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 643 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C VAL C 643 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL C 643 " -0.023 2.00e-02 2.50e+03 pdb=" N SER C 644 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 683 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO E 684 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 684 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 684 " 0.045 5.00e-02 4.00e+02 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1283 2.69 - 3.24: 32458 3.24 - 3.79: 54724 3.79 - 4.35: 68262 4.35 - 4.90: 109445 Nonbonded interactions: 266172 Sorted by model distance: nonbonded pdb=" O GLY F 608 " pdb=" O1B AGS F1001 " model vdw 2.132 2.432 nonbonded pdb=" O1B AGS E1001 " pdb=" O2A AGS E1001 " model vdw 2.173 2.440 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.223 2.440 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.225 2.440 nonbonded pdb=" O2A AGS B1001 " pdb=" O2B AGS B1001 " model vdw 2.226 2.440 ... (remaining 266167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858 or resid 1001)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858 or resid 1001)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 858 or resid 1001)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 858 or resid 1001)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 858 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.040 Extract box with map and model: 5.770 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 85.520 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.012 0.185 33285 Z= 0.755 Angle : 1.245 37.988 44929 Z= 0.660 Chirality : 0.062 0.427 5088 Planarity : 0.008 0.084 5869 Dihedral : 11.468 138.276 12968 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.25 % Favored : 90.73 % Rotamer: Outliers : 0.41 % Allowed : 1.28 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.11), residues: 4077 helix: -2.01 (0.08), residues: 2332 sheet: -2.84 (0.25), residues: 354 loop : -2.76 (0.14), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP E 543 HIS 0.018 0.003 HIS F 747 PHE 0.038 0.005 PHE B 709 TYR 0.068 0.003 TYR E 661 ARG 0.018 0.001 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1066 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 242 MET cc_start: 0.7907 (mmp) cc_final: 0.7433 (mmp) REVERT: A 318 GLU cc_start: 0.8139 (mp0) cc_final: 0.7858 (mp0) REVERT: A 631 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7305 (ttm-80) REVERT: A 645 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7738 (ttm110) REVERT: A 661 TYR cc_start: 0.7165 (t80) cc_final: 0.6848 (t80) REVERT: A 673 VAL cc_start: 0.9093 (t) cc_final: 0.8855 (p) REVERT: A 749 PHE cc_start: 0.7611 (m-10) cc_final: 0.7014 (m-10) REVERT: A 776 GLN cc_start: 0.8851 (mt0) cc_final: 0.8472 (tp40) REVERT: B 163 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8238 (mtmt) REVERT: B 201 ASN cc_start: 0.6805 (m-40) cc_final: 0.6524 (m-40) REVERT: B 265 ASP cc_start: 0.8429 (m-30) cc_final: 0.7798 (m-30) REVERT: B 275 LEU cc_start: 0.9535 (tp) cc_final: 0.9288 (tt) REVERT: B 299 LEU cc_start: 0.9181 (mp) cc_final: 0.8936 (mt) REVERT: B 310 CYS cc_start: 0.7110 (t) cc_final: 0.6484 (t) REVERT: B 430 MET cc_start: 0.3692 (mmm) cc_final: 0.3020 (ttm) REVERT: B 587 SER cc_start: 0.9014 (t) cc_final: 0.8786 (p) REVERT: B 615 CYS cc_start: 0.8367 (m) cc_final: 0.8098 (t) REVERT: B 627 GLU cc_start: 0.7659 (mp0) cc_final: 0.7290 (tm-30) REVERT: B 629 MET cc_start: 0.8030 (ptm) cc_final: 0.7624 (ppp) REVERT: B 634 MET cc_start: 0.8309 (mmm) cc_final: 0.8033 (mmm) REVERT: B 719 ASN cc_start: 0.8199 (p0) cc_final: 0.7885 (m110) REVERT: B 758 ASP cc_start: 0.7426 (t0) cc_final: 0.6848 (m-30) REVERT: B 821 ILE cc_start: 0.8869 (mt) cc_final: 0.8526 (mm) REVERT: B 846 LEU cc_start: 0.9372 (mt) cc_final: 0.9103 (tt) REVERT: C 196 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8017 (mtm-85) REVERT: C 246 VAL cc_start: 0.7622 (t) cc_final: 0.7281 (m) REVERT: C 257 GLU cc_start: 0.8554 (tt0) cc_final: 0.8092 (tm-30) REVERT: C 268 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8498 (tptt) REVERT: C 318 GLU cc_start: 0.8466 (mp0) cc_final: 0.7886 (mp0) REVERT: C 498 MET cc_start: 0.4996 (mmm) cc_final: 0.4714 (mmm) REVERT: C 602 LEU cc_start: 0.8887 (tp) cc_final: 0.8618 (tt) REVERT: C 615 CYS cc_start: 0.9154 (m) cc_final: 0.8361 (t) REVERT: C 638 MET cc_start: 0.8518 (mtm) cc_final: 0.8283 (mtm) REVERT: C 821 ILE cc_start: 0.8299 (mt) cc_final: 0.8098 (mm) REVERT: C 827 ASN cc_start: 0.9264 (m-40) cc_final: 0.8990 (m-40) REVERT: D 180 VAL cc_start: 0.8320 (t) cc_final: 0.8063 (p) REVERT: D 274 ILE cc_start: 0.8103 (mt) cc_final: 0.7782 (mm) REVERT: D 323 ILE cc_start: 0.8089 (mt) cc_final: 0.7881 (mm) REVERT: D 358 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7683 (pp20) REVERT: D 395 ASP cc_start: 0.8768 (t0) cc_final: 0.8269 (t0) REVERT: D 524 MET cc_start: 0.5121 (mmm) cc_final: 0.4587 (mmt) REVERT: D 630 VAL cc_start: 0.8618 (t) cc_final: 0.8312 (t) REVERT: D 691 LEU cc_start: 0.8101 (mt) cc_final: 0.7650 (mt) REVERT: D 760 VAL cc_start: 0.8492 (t) cc_final: 0.8000 (p) REVERT: D 774 ILE cc_start: 0.9058 (mt) cc_final: 0.8716 (tp) REVERT: D 792 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7616 (mp0) REVERT: D 834 LEU cc_start: 0.9041 (mt) cc_final: 0.8770 (mt) REVERT: E 319 TYR cc_start: 0.8508 (t80) cc_final: 0.8218 (t80) REVERT: E 335 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8246 (tptp) REVERT: E 370 ILE cc_start: 0.8177 (mt) cc_final: 0.7900 (mt) REVERT: E 540 LEU cc_start: 0.8636 (tp) cc_final: 0.8419 (tt) REVERT: E 562 MET cc_start: 0.8432 (tpt) cc_final: 0.8181 (tpt) REVERT: E 591 LEU cc_start: 0.8535 (mp) cc_final: 0.8313 (mp) REVERT: E 621 PHE cc_start: 0.8223 (t80) cc_final: 0.7818 (t80) REVERT: E 691 LEU cc_start: 0.8476 (mt) cc_final: 0.7967 (tp) REVERT: E 701 ASP cc_start: 0.8802 (p0) cc_final: 0.8283 (p0) REVERT: E 784 LYS cc_start: 0.9177 (tttt) cc_final: 0.8940 (tmmt) REVERT: E 817 LEU cc_start: 0.8826 (tp) cc_final: 0.8612 (tp) REVERT: F 242 MET cc_start: 0.6249 (mmp) cc_final: 0.5812 (tpp) REVERT: F 319 TYR cc_start: 0.7514 (t80) cc_final: 0.6816 (t80) REVERT: F 322 TYR cc_start: 0.7298 (m-10) cc_final: 0.6911 (m-10) REVERT: F 324 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6168 (pp20) REVERT: F 333 PHE cc_start: 0.7355 (m-80) cc_final: 0.7153 (m-10) REVERT: F 456 SER cc_start: 0.9119 (t) cc_final: 0.8764 (p) REVERT: F 457 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8389 (tm-30) REVERT: F 462 TRP cc_start: 0.7601 (t60) cc_final: 0.6523 (t60) REVERT: F 476 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7156 (tptp) REVERT: F 603 PHE cc_start: 0.7742 (m-10) cc_final: 0.7181 (m-10) REVERT: F 613 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8063 (tt0) REVERT: F 614 LEU cc_start: 0.8421 (tp) cc_final: 0.8087 (mt) REVERT: F 797 ASP cc_start: 0.8109 (m-30) cc_final: 0.7901 (p0) REVERT: F 801 LYS cc_start: 0.9394 (mtpp) cc_final: 0.8953 (mttt) outliers start: 14 outliers final: 3 residues processed: 1079 average time/residue: 0.5090 time to fit residues: 836.0657 Evaluate side-chains 576 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 320 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 371 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 334 GLN B 770 HIS B 831 GLN B 858 HIS C 192 GLN C 454 GLN C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN C 822 GLN ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 HIS D 281 HIS D 512 GLN D 641 HIS D 747 HIS D 823 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN E 297 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 822 GLN ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS F 688 ASN F 778 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 33285 Z= 0.236 Angle : 0.733 16.649 44929 Z= 0.368 Chirality : 0.044 0.300 5088 Planarity : 0.006 0.065 5869 Dihedral : 9.770 136.899 4748 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.12), residues: 4077 helix: -0.55 (0.10), residues: 2317 sheet: -2.74 (0.24), residues: 351 loop : -2.24 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 543 HIS 0.007 0.001 HIS D 747 PHE 0.018 0.002 PHE F 637 TYR 0.022 0.002 TYR C 653 ARG 0.022 0.001 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 741 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 241 ASP cc_start: 0.8558 (t0) cc_final: 0.8177 (t0) REVERT: A 276 PHE cc_start: 0.7852 (t80) cc_final: 0.7503 (t80) REVERT: A 631 ARG cc_start: 0.8243 (ttt180) cc_final: 0.7379 (ttm-80) REVERT: A 673 VAL cc_start: 0.9128 (t) cc_final: 0.8335 (p) REVERT: A 716 MET cc_start: 0.8756 (mpp) cc_final: 0.8490 (mpp) REVERT: A 749 PHE cc_start: 0.7012 (m-10) cc_final: 0.6597 (m-10) REVERT: A 776 GLN cc_start: 0.8801 (mt0) cc_final: 0.8571 (tp40) REVERT: B 163 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8186 (mttt) REVERT: B 170 GLU cc_start: 0.8851 (tt0) cc_final: 0.8490 (tp30) REVERT: B 201 ASN cc_start: 0.7208 (m-40) cc_final: 0.6771 (m-40) REVERT: B 207 GLU cc_start: 0.8579 (mp0) cc_final: 0.8356 (mm-30) REVERT: B 361 HIS cc_start: 0.6922 (m-70) cc_final: 0.6705 (m-70) REVERT: B 403 MET cc_start: 0.7574 (mmt) cc_final: 0.7374 (mmm) REVERT: B 430 MET cc_start: 0.3401 (mmm) cc_final: 0.2166 (tmm) REVERT: B 531 VAL cc_start: 0.8663 (t) cc_final: 0.8388 (t) REVERT: B 587 SER cc_start: 0.9061 (t) cc_final: 0.8741 (p) REVERT: B 615 CYS cc_start: 0.8213 (m) cc_final: 0.7994 (t) REVERT: B 629 MET cc_start: 0.8230 (ptm) cc_final: 0.7948 (ppp) REVERT: B 633 ASP cc_start: 0.8293 (p0) cc_final: 0.7957 (p0) REVERT: B 719 ASN cc_start: 0.8136 (p0) cc_final: 0.7645 (m110) REVERT: B 758 ASP cc_start: 0.7553 (t0) cc_final: 0.6841 (m-30) REVERT: B 782 LEU cc_start: 0.9492 (tp) cc_final: 0.9228 (tt) REVERT: B 791 TYR cc_start: 0.6736 (m-80) cc_final: 0.6447 (m-10) REVERT: B 846 LEU cc_start: 0.9475 (mt) cc_final: 0.9166 (tt) REVERT: C 232 LEU cc_start: 0.9028 (mt) cc_final: 0.8822 (mt) REVERT: C 257 GLU cc_start: 0.8264 (tt0) cc_final: 0.7867 (tm-30) REVERT: C 260 LYS cc_start: 0.8369 (tttt) cc_final: 0.7915 (mmtt) REVERT: C 388 ASP cc_start: 0.8232 (t70) cc_final: 0.7953 (t0) REVERT: C 430 MET cc_start: -0.0328 (ppp) cc_final: -0.1322 (tpt) REVERT: C 498 MET cc_start: 0.5018 (mmm) cc_final: 0.4714 (mmm) REVERT: C 595 ASN cc_start: 0.8338 (m-40) cc_final: 0.7632 (p0) REVERT: C 724 LEU cc_start: 0.8665 (tp) cc_final: 0.8274 (tp) REVERT: C 757 ILE cc_start: 0.9166 (mm) cc_final: 0.8886 (tp) REVERT: C 827 ASN cc_start: 0.9351 (m-40) cc_final: 0.9149 (m-40) REVERT: D 180 VAL cc_start: 0.8544 (t) cc_final: 0.8302 (p) REVERT: D 358 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7685 (pp20) REVERT: D 396 GLU cc_start: 0.8812 (tp30) cc_final: 0.8458 (tp30) REVERT: D 524 MET cc_start: 0.5032 (mmm) cc_final: 0.4552 (mmt) REVERT: D 691 LEU cc_start: 0.8047 (mt) cc_final: 0.7117 (mt) REVERT: D 736 HIS cc_start: 0.8520 (m170) cc_final: 0.8068 (m170) REVERT: D 774 ILE cc_start: 0.9188 (mt) cc_final: 0.8823 (tp) REVERT: E 319 TYR cc_start: 0.8438 (t80) cc_final: 0.8179 (t80) REVERT: E 335 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8547 (tptp) REVERT: E 495 LEU cc_start: 0.6994 (tt) cc_final: 0.6540 (mm) REVERT: E 562 MET cc_start: 0.8588 (tpt) cc_final: 0.8219 (tpp) REVERT: E 621 PHE cc_start: 0.8223 (t80) cc_final: 0.7720 (t80) REVERT: E 780 LYS cc_start: 0.8647 (mptt) cc_final: 0.8437 (mmtm) REVERT: E 784 LYS cc_start: 0.9140 (tttt) cc_final: 0.8916 (ttpt) REVERT: F 242 MET cc_start: 0.5848 (mmp) cc_final: 0.5493 (tpt) REVERT: F 319 TYR cc_start: 0.7611 (t80) cc_final: 0.7289 (t80) REVERT: F 324 GLU cc_start: 0.6411 (mt-10) cc_final: 0.5974 (tp30) REVERT: F 381 ILE cc_start: 0.7848 (mp) cc_final: 0.7573 (mp) REVERT: F 462 TRP cc_start: 0.7688 (t60) cc_final: 0.6510 (t60) REVERT: F 498 MET cc_start: 0.6645 (tpp) cc_final: 0.6271 (tpp) REVERT: F 512 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6429 (pt0) REVERT: F 556 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7816 (tmm160) REVERT: F 564 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7908 (tp-100) REVERT: F 613 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8172 (tt0) REVERT: F 614 LEU cc_start: 0.8338 (tp) cc_final: 0.7981 (mt) REVERT: F 696 ASP cc_start: 0.7213 (m-30) cc_final: 0.6448 (t0) REVERT: F 716 MET cc_start: 0.9259 (mpp) cc_final: 0.8949 (mpp) REVERT: F 758 ASP cc_start: 0.5109 (t0) cc_final: 0.4613 (m-30) REVERT: F 777 ILE cc_start: 0.8391 (mt) cc_final: 0.7973 (mt) REVERT: F 801 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9062 (mtpt) outliers start: 6 outliers final: 2 residues processed: 745 average time/residue: 0.4681 time to fit residues: 548.2664 Evaluate side-chains 498 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 496 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 331 optimal weight: 8.9990 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS A 806 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN C 806 ASN ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 849 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 824 GLN F 192 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 HIS ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33285 Z= 0.237 Angle : 0.679 15.851 44929 Z= 0.342 Chirality : 0.043 0.207 5088 Planarity : 0.005 0.111 5869 Dihedral : 9.300 136.258 4748 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4077 helix: 0.12 (0.10), residues: 2332 sheet: -2.40 (0.24), residues: 376 loop : -2.06 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 462 HIS 0.013 0.001 HIS C 378 PHE 0.022 0.002 PHE F 621 TYR 0.017 0.001 TYR C 653 ARG 0.009 0.001 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 640 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7859 (mmm) cc_final: 0.7110 (mmm) REVERT: A 276 PHE cc_start: 0.7802 (t80) cc_final: 0.7543 (t80) REVERT: A 293 MET cc_start: 0.3121 (tpp) cc_final: 0.2669 (mmm) REVERT: A 318 GLU cc_start: 0.8149 (mp0) cc_final: 0.7936 (mp0) REVERT: A 403 MET cc_start: 0.7079 (ttt) cc_final: 0.6713 (ttt) REVERT: A 498 MET cc_start: 0.1112 (mmm) cc_final: 0.0837 (mtt) REVERT: A 508 GLU cc_start: 0.3356 (pt0) cc_final: 0.3138 (mt-10) REVERT: A 588 ARG cc_start: 0.7284 (mmt90) cc_final: 0.6868 (tmt170) REVERT: A 631 ARG cc_start: 0.8276 (ttt180) cc_final: 0.7369 (ttm-80) REVERT: A 673 VAL cc_start: 0.9166 (t) cc_final: 0.8334 (p) REVERT: A 714 VAL cc_start: 0.8265 (t) cc_final: 0.7906 (p) REVERT: A 717 THR cc_start: 0.8355 (p) cc_final: 0.8135 (p) REVERT: A 749 PHE cc_start: 0.7060 (m-10) cc_final: 0.6668 (m-10) REVERT: A 776 GLN cc_start: 0.8836 (mt0) cc_final: 0.8552 (tp40) REVERT: B 163 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8274 (mttt) REVERT: B 170 GLU cc_start: 0.8833 (tt0) cc_final: 0.8556 (tp30) REVERT: B 283 MET cc_start: 0.8143 (tpp) cc_final: 0.7935 (tpp) REVERT: B 310 CYS cc_start: 0.7778 (t) cc_final: 0.7547 (t) REVERT: B 349 ILE cc_start: 0.9099 (mm) cc_final: 0.8845 (mm) REVERT: B 361 HIS cc_start: 0.7418 (m-70) cc_final: 0.7060 (m-70) REVERT: B 403 MET cc_start: 0.7518 (mmt) cc_final: 0.7301 (mmm) REVERT: B 430 MET cc_start: 0.3434 (mmm) cc_final: 0.2225 (tmm) REVERT: B 638 MET cc_start: 0.8263 (mmt) cc_final: 0.7936 (mmt) REVERT: B 675 LEU cc_start: 0.9323 (tp) cc_final: 0.9090 (tt) REVERT: B 719 ASN cc_start: 0.8235 (p0) cc_final: 0.7728 (m110) REVERT: B 758 ASP cc_start: 0.8005 (t0) cc_final: 0.7045 (m-30) REVERT: B 782 LEU cc_start: 0.9499 (tp) cc_final: 0.9250 (tp) REVERT: B 791 TYR cc_start: 0.6653 (m-80) cc_final: 0.6254 (m-80) REVERT: B 846 LEU cc_start: 0.9528 (mt) cc_final: 0.9186 (tt) REVERT: C 177 LEU cc_start: 0.8807 (tp) cc_final: 0.8479 (tp) REVERT: C 232 LEU cc_start: 0.9073 (mt) cc_final: 0.8740 (mt) REVERT: C 257 GLU cc_start: 0.8492 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 260 LYS cc_start: 0.8364 (tttt) cc_final: 0.7938 (mmtt) REVERT: C 388 ASP cc_start: 0.8123 (t70) cc_final: 0.7920 (t0) REVERT: C 396 GLU cc_start: 0.8542 (tp30) cc_final: 0.8247 (tp30) REVERT: C 498 MET cc_start: 0.4992 (mmm) cc_final: 0.4683 (mmm) REVERT: C 524 MET cc_start: 0.1152 (ttt) cc_final: 0.0894 (ttp) REVERT: C 595 ASN cc_start: 0.8415 (m-40) cc_final: 0.7528 (p0) REVERT: C 615 CYS cc_start: 0.9194 (m) cc_final: 0.8645 (t) REVERT: C 633 ASP cc_start: 0.7776 (t0) cc_final: 0.7453 (t0) REVERT: C 724 LEU cc_start: 0.8666 (tp) cc_final: 0.8252 (tp) REVERT: C 827 ASN cc_start: 0.9350 (m-40) cc_final: 0.9141 (m-40) REVERT: D 204 LEU cc_start: 0.9149 (mm) cc_final: 0.8817 (mm) REVERT: D 358 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7841 (mt-10) REVERT: D 396 GLU cc_start: 0.8895 (tp30) cc_final: 0.8508 (tp30) REVERT: D 524 MET cc_start: 0.5147 (mmm) cc_final: 0.4618 (mmt) REVERT: D 725 ILE cc_start: 0.9196 (mt) cc_final: 0.8983 (mt) REVERT: D 774 ILE cc_start: 0.9275 (mt) cc_final: 0.8942 (tp) REVERT: E 319 TYR cc_start: 0.8656 (t80) cc_final: 0.8425 (t80) REVERT: E 535 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7663 (tp30) REVERT: E 562 MET cc_start: 0.8510 (tpt) cc_final: 0.8226 (tpp) REVERT: E 621 PHE cc_start: 0.8248 (t80) cc_final: 0.7671 (t80) REVERT: E 638 MET cc_start: 0.8166 (pmm) cc_final: 0.7199 (ptp) REVERT: E 817 LEU cc_start: 0.9048 (tp) cc_final: 0.8565 (tp) REVERT: E 821 ILE cc_start: 0.8588 (mm) cc_final: 0.8304 (pt) REVERT: F 298 MET cc_start: 0.6459 (mmp) cc_final: 0.6245 (mmm) REVERT: F 324 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6006 (tp30) REVERT: F 456 SER cc_start: 0.8871 (p) cc_final: 0.8670 (p) REVERT: F 498 MET cc_start: 0.6539 (tpp) cc_final: 0.6152 (tpp) REVERT: F 512 GLN cc_start: 0.7327 (tm-30) cc_final: 0.6527 (pt0) REVERT: F 556 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7815 (tmm160) REVERT: F 613 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8260 (tt0) REVERT: F 614 LEU cc_start: 0.8379 (tp) cc_final: 0.7948 (mt) REVERT: F 696 ASP cc_start: 0.6546 (m-30) cc_final: 0.5806 (t0) REVERT: F 716 MET cc_start: 0.9307 (mpp) cc_final: 0.8905 (mpp) REVERT: F 758 ASP cc_start: 0.5034 (t0) cc_final: 0.4552 (m-30) REVERT: F 801 LYS cc_start: 0.9422 (mtpp) cc_final: 0.9020 (mtpt) REVERT: F 821 ILE cc_start: 0.8511 (tp) cc_final: 0.8285 (tp) outliers start: 2 outliers final: 2 residues processed: 642 average time/residue: 0.4398 time to fit residues: 458.5031 Evaluate side-chains 450 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 448 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 395 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 353 optimal weight: 0.0570 chunk 106 optimal weight: 10.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 770 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 824 GLN ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 688 ASN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33285 Z= 0.198 Angle : 0.637 14.959 44929 Z= 0.320 Chirality : 0.042 0.152 5088 Planarity : 0.005 0.076 5869 Dihedral : 9.018 138.175 4748 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.78 (0.13), residues: 4077 helix: 0.57 (0.11), residues: 2326 sheet: -2.14 (0.25), residues: 383 loop : -1.84 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 462 HIS 0.004 0.001 HIS D 362 PHE 0.023 0.002 PHE F 709 TYR 0.017 0.001 TYR A 357 ARG 0.013 0.001 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 607 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8187 (m-40) cc_final: 0.7653 (m-40) REVERT: A 241 ASP cc_start: 0.8400 (t0) cc_final: 0.8149 (t0) REVERT: A 242 MET cc_start: 0.7887 (mmm) cc_final: 0.7222 (mmm) REVERT: A 293 MET cc_start: 0.4089 (tpp) cc_final: 0.3297 (mmm) REVERT: A 318 GLU cc_start: 0.8251 (mp0) cc_final: 0.7960 (mp0) REVERT: A 344 GLU cc_start: 0.9209 (pm20) cc_final: 0.8914 (pm20) REVERT: A 588 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6998 (tmt170) REVERT: A 631 ARG cc_start: 0.8370 (ttt180) cc_final: 0.7456 (ttm-80) REVERT: A 673 VAL cc_start: 0.9221 (t) cc_final: 0.8578 (p) REVERT: A 714 VAL cc_start: 0.8431 (t) cc_final: 0.8074 (p) REVERT: A 717 THR cc_start: 0.8338 (p) cc_final: 0.8052 (p) REVERT: A 749 PHE cc_start: 0.7171 (m-10) cc_final: 0.6755 (m-10) REVERT: A 776 GLN cc_start: 0.8861 (mt0) cc_final: 0.8481 (tp40) REVERT: A 779 LEU cc_start: 0.8333 (mt) cc_final: 0.8038 (mt) REVERT: A 783 TYR cc_start: 0.8726 (m-10) cc_final: 0.8417 (m-80) REVERT: B 170 GLU cc_start: 0.8831 (tt0) cc_final: 0.8587 (tp30) REVERT: B 283 MET cc_start: 0.8169 (tpp) cc_final: 0.7954 (tpp) REVERT: B 310 CYS cc_start: 0.7639 (t) cc_final: 0.7433 (t) REVERT: B 361 HIS cc_start: 0.7566 (m-70) cc_final: 0.7212 (m-70) REVERT: B 403 MET cc_start: 0.7503 (mmt) cc_final: 0.7270 (mmm) REVERT: B 430 MET cc_start: 0.3205 (mmm) cc_final: 0.2085 (tmm) REVERT: B 629 MET cc_start: 0.8266 (ppp) cc_final: 0.7918 (ppp) REVERT: B 638 MET cc_start: 0.8311 (mmt) cc_final: 0.8083 (mmt) REVERT: B 719 ASN cc_start: 0.8232 (p0) cc_final: 0.7751 (m110) REVERT: B 758 ASP cc_start: 0.8257 (t0) cc_final: 0.7388 (m-30) REVERT: B 782 LEU cc_start: 0.9464 (tp) cc_final: 0.9191 (tp) REVERT: B 791 TYR cc_start: 0.6542 (m-80) cc_final: 0.6100 (m-80) REVERT: B 846 LEU cc_start: 0.9561 (mt) cc_final: 0.9213 (tt) REVERT: C 177 LEU cc_start: 0.8947 (tp) cc_final: 0.8601 (tp) REVERT: C 196 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.8083 (mtm-85) REVERT: C 232 LEU cc_start: 0.8933 (mt) cc_final: 0.8632 (mt) REVERT: C 257 GLU cc_start: 0.8528 (tt0) cc_final: 0.8013 (tm-30) REVERT: C 300 LYS cc_start: 0.9017 (tppt) cc_final: 0.8284 (mmmm) REVERT: C 388 ASP cc_start: 0.8170 (t70) cc_final: 0.7956 (t0) REVERT: C 396 GLU cc_start: 0.8652 (tp30) cc_final: 0.8363 (tp30) REVERT: C 498 MET cc_start: 0.4995 (mmm) cc_final: 0.4679 (mmm) REVERT: C 524 MET cc_start: 0.1264 (ttt) cc_final: 0.0960 (ttp) REVERT: C 595 ASN cc_start: 0.8423 (m-40) cc_final: 0.7403 (p0) REVERT: C 615 CYS cc_start: 0.9219 (m) cc_final: 0.8766 (t) REVERT: C 633 ASP cc_start: 0.7533 (t0) cc_final: 0.7143 (t0) REVERT: C 639 GLU cc_start: 0.7971 (pm20) cc_final: 0.7708 (pm20) REVERT: C 716 MET cc_start: 0.8235 (mtp) cc_final: 0.7478 (ttm) REVERT: C 758 ASP cc_start: 0.8681 (t0) cc_final: 0.8417 (m-30) REVERT: C 827 ASN cc_start: 0.9345 (m-40) cc_final: 0.9135 (m-40) REVERT: D 242 MET cc_start: 0.7944 (mmm) cc_final: 0.7679 (mmm) REVERT: D 392 ASP cc_start: 0.7819 (m-30) cc_final: 0.7502 (m-30) REVERT: D 396 GLU cc_start: 0.8937 (tp30) cc_final: 0.8516 (tp30) REVERT: D 524 MET cc_start: 0.5126 (mmm) cc_final: 0.4597 (mmt) REVERT: D 691 LEU cc_start: 0.8193 (mt) cc_final: 0.7798 (mt) REVERT: D 774 ILE cc_start: 0.9336 (mt) cc_final: 0.8940 (tp) REVERT: E 195 GLN cc_start: 0.7714 (pt0) cc_final: 0.7162 (mm-40) REVERT: E 283 MET cc_start: 0.8709 (tmm) cc_final: 0.8435 (tmm) REVERT: E 319 TYR cc_start: 0.8572 (t80) cc_final: 0.8220 (t80) REVERT: E 370 ILE cc_start: 0.8584 (mt) cc_final: 0.8369 (mt) REVERT: E 535 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7660 (tp30) REVERT: E 601 PHE cc_start: 0.8253 (m-80) cc_final: 0.7745 (m-10) REVERT: E 638 MET cc_start: 0.8273 (pmm) cc_final: 0.7532 (ptm) REVERT: E 817 LEU cc_start: 0.9138 (tp) cc_final: 0.8865 (tp) REVERT: E 853 ILE cc_start: 0.8549 (tt) cc_final: 0.8286 (mm) REVERT: F 319 TYR cc_start: 0.7772 (t80) cc_final: 0.7569 (t80) REVERT: F 324 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6319 (tp30) REVERT: F 498 MET cc_start: 0.6528 (tpp) cc_final: 0.6171 (tpp) REVERT: F 556 ARG cc_start: 0.8203 (tpp-160) cc_final: 0.7781 (tmm160) REVERT: F 562 MET cc_start: 0.7781 (tmm) cc_final: 0.7499 (tmm) REVERT: F 613 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8314 (tt0) REVERT: F 614 LEU cc_start: 0.8424 (tp) cc_final: 0.7977 (mt) REVERT: F 716 MET cc_start: 0.9288 (mpp) cc_final: 0.8888 (mpp) REVERT: F 758 ASP cc_start: 0.4841 (t0) cc_final: 0.4438 (m-30) outliers start: 2 outliers final: 0 residues processed: 608 average time/residue: 0.4319 time to fit residues: 429.5337 Evaluate side-chains 441 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 337 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.5980 chunk 354 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN C 832 GLN C 849 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 GLN D 824 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN F 770 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33285 Z= 0.232 Angle : 0.663 14.503 44929 Z= 0.331 Chirality : 0.042 0.189 5088 Planarity : 0.005 0.057 5869 Dihedral : 8.919 141.030 4748 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.13), residues: 4077 helix: 0.76 (0.11), residues: 2327 sheet: -2.07 (0.25), residues: 384 loop : -1.78 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 543 HIS 0.013 0.001 HIS D 747 PHE 0.021 0.002 PHE E 621 TYR 0.016 0.001 TYR C 653 ARG 0.009 0.001 ARG E 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 577 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8244 (m-40) cc_final: 0.7707 (m-40) REVERT: A 241 ASP cc_start: 0.8315 (t0) cc_final: 0.8075 (t0) REVERT: A 242 MET cc_start: 0.7908 (mmm) cc_final: 0.7451 (mmm) REVERT: A 246 VAL cc_start: 0.7402 (t) cc_final: 0.7125 (t) REVERT: A 293 MET cc_start: 0.4104 (tpp) cc_final: 0.3358 (mmt) REVERT: A 318 GLU cc_start: 0.8269 (mp0) cc_final: 0.7882 (mp0) REVERT: A 459 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 588 ARG cc_start: 0.7585 (mmt90) cc_final: 0.7166 (tmt170) REVERT: A 631 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7366 (ttm-80) REVERT: A 714 VAL cc_start: 0.8616 (t) cc_final: 0.8303 (p) REVERT: A 717 THR cc_start: 0.8260 (p) cc_final: 0.8032 (p) REVERT: A 749 PHE cc_start: 0.7252 (m-10) cc_final: 0.6813 (m-10) REVERT: A 776 GLN cc_start: 0.8898 (mt0) cc_final: 0.8547 (tp40) REVERT: A 802 LEU cc_start: 0.5549 (pp) cc_final: 0.5141 (mt) REVERT: B 170 GLU cc_start: 0.8833 (tt0) cc_final: 0.8541 (tp30) REVERT: B 186 GLU cc_start: 0.8343 (mp0) cc_final: 0.7875 (mp0) REVERT: B 361 HIS cc_start: 0.7618 (m-70) cc_final: 0.6759 (m-70) REVERT: B 403 MET cc_start: 0.7634 (mmt) cc_final: 0.7355 (mmm) REVERT: B 430 MET cc_start: 0.3101 (mmm) cc_final: 0.2054 (tmm) REVERT: B 629 MET cc_start: 0.8364 (ppp) cc_final: 0.8036 (ppp) REVERT: B 719 ASN cc_start: 0.8349 (p0) cc_final: 0.7758 (m110) REVERT: B 758 ASP cc_start: 0.8355 (t0) cc_final: 0.7380 (m-30) REVERT: B 782 LEU cc_start: 0.9437 (tp) cc_final: 0.9076 (tp) REVERT: B 791 TYR cc_start: 0.6523 (m-80) cc_final: 0.6161 (m-80) REVERT: B 846 LEU cc_start: 0.9532 (mt) cc_final: 0.9248 (tt) REVERT: C 177 LEU cc_start: 0.8989 (tp) cc_final: 0.8602 (tp) REVERT: C 196 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8187 (mtm-85) REVERT: C 232 LEU cc_start: 0.8931 (mt) cc_final: 0.8649 (mt) REVERT: C 257 GLU cc_start: 0.8667 (tt0) cc_final: 0.8110 (tm-30) REVERT: C 317 ASP cc_start: 0.8715 (m-30) cc_final: 0.8403 (t0) REVERT: C 396 GLU cc_start: 0.8636 (tp30) cc_final: 0.8359 (tp30) REVERT: C 403 MET cc_start: 0.9095 (tpp) cc_final: 0.8769 (tpp) REVERT: C 498 MET cc_start: 0.5071 (mmm) cc_final: 0.4749 (mmm) REVERT: C 535 GLU cc_start: 0.8657 (mp0) cc_final: 0.8281 (mp0) REVERT: C 595 ASN cc_start: 0.8460 (m-40) cc_final: 0.7551 (p0) REVERT: C 601 PHE cc_start: 0.8745 (m-80) cc_final: 0.8127 (m-80) REVERT: C 613 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8472 (mm-30) REVERT: C 615 CYS cc_start: 0.9251 (m) cc_final: 0.8762 (t) REVERT: C 639 GLU cc_start: 0.8200 (pm20) cc_final: 0.7909 (pm20) REVERT: C 716 MET cc_start: 0.8278 (mtp) cc_final: 0.7439 (ttm) REVERT: C 827 ASN cc_start: 0.9381 (m-40) cc_final: 0.9140 (m-40) REVERT: D 204 LEU cc_start: 0.9301 (mm) cc_final: 0.9042 (mm) REVERT: D 358 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7668 (mm-30) REVERT: D 396 GLU cc_start: 0.8985 (tp30) cc_final: 0.8570 (tp30) REVERT: D 524 MET cc_start: 0.5245 (mmm) cc_final: 0.4633 (mmt) REVERT: D 691 LEU cc_start: 0.8127 (mt) cc_final: 0.7720 (mt) REVERT: E 195 GLN cc_start: 0.7835 (pt0) cc_final: 0.7245 (mm-40) REVERT: E 217 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6956 (tt0) REVERT: E 254 GLU cc_start: 0.7021 (mp0) cc_final: 0.6739 (mp0) REVERT: E 283 MET cc_start: 0.8776 (tmm) cc_final: 0.8528 (tmm) REVERT: E 319 TYR cc_start: 0.8633 (t80) cc_final: 0.8264 (t80) REVERT: E 475 ILE cc_start: 0.7828 (pt) cc_final: 0.7528 (pt) REVERT: E 535 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7502 (tp30) REVERT: E 562 MET cc_start: 0.8394 (tpp) cc_final: 0.8113 (tpt) REVERT: E 601 PHE cc_start: 0.8296 (m-80) cc_final: 0.7831 (m-10) REVERT: E 638 MET cc_start: 0.8350 (pmm) cc_final: 0.7594 (ptm) REVERT: E 642 SER cc_start: 0.8367 (m) cc_final: 0.7214 (p) REVERT: E 817 LEU cc_start: 0.9173 (tp) cc_final: 0.8885 (tp) REVERT: F 319 TYR cc_start: 0.7727 (t80) cc_final: 0.7482 (t80) REVERT: F 324 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6454 (tp30) REVERT: F 556 ARG cc_start: 0.8325 (tpp-160) cc_final: 0.7749 (tmm160) REVERT: F 613 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8401 (tt0) REVERT: F 614 LEU cc_start: 0.8455 (tp) cc_final: 0.8022 (mt) REVERT: F 716 MET cc_start: 0.9293 (mpp) cc_final: 0.8893 (mpp) REVERT: F 737 MET cc_start: 0.7799 (mmm) cc_final: 0.7521 (tpp) outliers start: 1 outliers final: 0 residues processed: 577 average time/residue: 0.4380 time to fit residues: 411.1983 Evaluate side-chains 421 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 0.7980 chunk 356 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 232 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 395 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 806 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33285 Z= 0.229 Angle : 0.654 14.417 44929 Z= 0.328 Chirality : 0.043 0.217 5088 Planarity : 0.004 0.057 5869 Dihedral : 8.876 143.661 4748 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.38 (0.13), residues: 4077 helix: 0.89 (0.11), residues: 2325 sheet: -1.94 (0.25), residues: 394 loop : -1.67 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 543 HIS 0.007 0.001 HIS E 641 PHE 0.024 0.002 PHE F 621 TYR 0.030 0.001 TYR F 656 ARG 0.013 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 567 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8340 (m-40) cc_final: 0.7855 (m-40) REVERT: A 241 ASP cc_start: 0.8270 (t0) cc_final: 0.7990 (t0) REVERT: A 242 MET cc_start: 0.7836 (mmm) cc_final: 0.7137 (mmm) REVERT: A 276 PHE cc_start: 0.7682 (t80) cc_final: 0.7420 (t80) REVERT: A 293 MET cc_start: 0.3723 (tpp) cc_final: 0.3157 (mmt) REVERT: A 318 GLU cc_start: 0.8203 (mp0) cc_final: 0.7746 (mp0) REVERT: A 459 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 588 ARG cc_start: 0.7673 (mmt90) cc_final: 0.7204 (tmt170) REVERT: A 624 ASP cc_start: 0.7624 (m-30) cc_final: 0.7109 (p0) REVERT: A 631 ARG cc_start: 0.8382 (ttt180) cc_final: 0.7362 (ttm-80) REVERT: A 714 VAL cc_start: 0.8784 (t) cc_final: 0.8481 (p) REVERT: A 717 THR cc_start: 0.8175 (p) cc_final: 0.7910 (p) REVERT: A 749 PHE cc_start: 0.7394 (m-10) cc_final: 0.6892 (m-10) REVERT: A 776 GLN cc_start: 0.8912 (mt0) cc_final: 0.8493 (tp40) REVERT: A 802 LEU cc_start: 0.5893 (pp) cc_final: 0.5392 (mt) REVERT: B 170 GLU cc_start: 0.8857 (tt0) cc_final: 0.8529 (tp30) REVERT: B 186 GLU cc_start: 0.8277 (mp0) cc_final: 0.7737 (mp0) REVERT: B 283 MET cc_start: 0.8265 (tpp) cc_final: 0.7750 (tpp) REVERT: B 403 MET cc_start: 0.7756 (mmt) cc_final: 0.7436 (mmm) REVERT: B 430 MET cc_start: 0.2829 (mmm) cc_final: 0.2189 (ttm) REVERT: B 629 MET cc_start: 0.8591 (ppp) cc_final: 0.8178 (ppp) REVERT: B 630 VAL cc_start: 0.9297 (m) cc_final: 0.8980 (m) REVERT: B 719 ASN cc_start: 0.8463 (p0) cc_final: 0.7794 (m110) REVERT: B 758 ASP cc_start: 0.8525 (t0) cc_final: 0.7445 (m-30) REVERT: B 759 GLU cc_start: 0.8086 (tt0) cc_final: 0.7439 (tt0) REVERT: B 782 LEU cc_start: 0.9447 (tp) cc_final: 0.9185 (tp) REVERT: B 846 LEU cc_start: 0.9481 (mt) cc_final: 0.9234 (tt) REVERT: C 177 LEU cc_start: 0.9012 (tp) cc_final: 0.8627 (tp) REVERT: C 196 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8104 (mtm-85) REVERT: C 232 LEU cc_start: 0.8891 (mt) cc_final: 0.8613 (mt) REVERT: C 257 GLU cc_start: 0.8710 (tt0) cc_final: 0.8136 (tm-30) REVERT: C 317 ASP cc_start: 0.8757 (m-30) cc_final: 0.8352 (t0) REVERT: C 396 GLU cc_start: 0.8655 (tp30) cc_final: 0.8407 (tp30) REVERT: C 498 MET cc_start: 0.5153 (mmm) cc_final: 0.4839 (mmm) REVERT: C 524 MET cc_start: 0.1217 (ttt) cc_final: 0.0911 (ttp) REVERT: C 581 SER cc_start: 0.8487 (m) cc_final: 0.8142 (p) REVERT: C 595 ASN cc_start: 0.8517 (m-40) cc_final: 0.7696 (p0) REVERT: C 615 CYS cc_start: 0.9235 (m) cc_final: 0.8760 (t) REVERT: C 633 ASP cc_start: 0.7707 (t0) cc_final: 0.7373 (t0) REVERT: C 716 MET cc_start: 0.8255 (mtp) cc_final: 0.7477 (ttm) REVERT: C 821 ILE cc_start: 0.8205 (mt) cc_final: 0.7540 (mt) REVERT: C 827 ASN cc_start: 0.9363 (m-40) cc_final: 0.9069 (m-40) REVERT: D 191 ILE cc_start: 0.7817 (mm) cc_final: 0.7144 (mm) REVERT: D 192 GLN cc_start: 0.8943 (mt0) cc_final: 0.8431 (mt0) REVERT: D 204 LEU cc_start: 0.9312 (mm) cc_final: 0.9081 (mm) REVERT: D 358 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7169 (mm-30) REVERT: D 396 GLU cc_start: 0.8996 (tp30) cc_final: 0.8568 (tp30) REVERT: D 524 MET cc_start: 0.5251 (mmm) cc_final: 0.4596 (mmt) REVERT: D 691 LEU cc_start: 0.8067 (mt) cc_final: 0.7636 (mt) REVERT: E 195 GLN cc_start: 0.7879 (pt0) cc_final: 0.7376 (mm-40) REVERT: E 217 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7086 (tt0) REVERT: E 254 GLU cc_start: 0.7249 (mp0) cc_final: 0.6942 (mp0) REVERT: E 283 MET cc_start: 0.8799 (tmm) cc_final: 0.8567 (tmm) REVERT: E 319 TYR cc_start: 0.8657 (t80) cc_final: 0.8302 (t80) REVERT: E 443 MET cc_start: 0.5885 (tmm) cc_final: 0.3802 (mtt) REVERT: E 475 ILE cc_start: 0.7790 (pt) cc_final: 0.7473 (pt) REVERT: E 562 MET cc_start: 0.8045 (tpp) cc_final: 0.7726 (tpp) REVERT: E 601 PHE cc_start: 0.8289 (m-80) cc_final: 0.8058 (m-80) REVERT: E 638 MET cc_start: 0.8181 (pmm) cc_final: 0.7708 (ptm) REVERT: E 642 SER cc_start: 0.8693 (m) cc_final: 0.7481 (p) REVERT: E 687 PHE cc_start: 0.8522 (m-10) cc_final: 0.7944 (m-80) REVERT: E 817 LEU cc_start: 0.9239 (tp) cc_final: 0.8973 (tp) REVERT: F 319 TYR cc_start: 0.7815 (t80) cc_final: 0.7426 (t80) REVERT: F 324 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6258 (tp30) REVERT: F 498 MET cc_start: 0.6225 (tpp) cc_final: 0.5781 (tpp) REVERT: F 512 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6319 (mt0) REVERT: F 556 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.7785 (tmm160) REVERT: F 613 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8418 (tt0) REVERT: F 614 LEU cc_start: 0.8649 (tp) cc_final: 0.8260 (mt) REVERT: F 716 MET cc_start: 0.9260 (mpp) cc_final: 0.8890 (mpp) REVERT: F 737 MET cc_start: 0.7824 (mmm) cc_final: 0.7574 (tpp) REVERT: F 763 PHE cc_start: 0.7943 (m-80) cc_final: 0.7724 (m-80) REVERT: F 777 ILE cc_start: 0.8376 (mt) cc_final: 0.7913 (mt) REVERT: F 780 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8504 (mtmm) outliers start: 1 outliers final: 0 residues processed: 567 average time/residue: 0.4221 time to fit residues: 393.7090 Evaluate side-chains 396 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 394 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 182 optimal weight: 0.3980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 281 HIS D 488 GLN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33285 Z= 0.227 Angle : 0.656 14.338 44929 Z= 0.326 Chirality : 0.043 0.167 5088 Planarity : 0.004 0.050 5869 Dihedral : 8.816 143.803 4748 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4077 helix: 0.99 (0.11), residues: 2321 sheet: -1.95 (0.25), residues: 387 loop : -1.61 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 543 HIS 0.006 0.001 HIS D 747 PHE 0.019 0.002 PHE F 621 TYR 0.021 0.001 TYR F 656 ARG 0.014 0.001 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8328 (m-40) cc_final: 0.7941 (m110) REVERT: A 241 ASP cc_start: 0.8326 (t0) cc_final: 0.8048 (t0) REVERT: A 242 MET cc_start: 0.7905 (mmm) cc_final: 0.7286 (mmm) REVERT: A 293 MET cc_start: 0.3663 (tpp) cc_final: 0.3104 (mmt) REVERT: A 318 GLU cc_start: 0.8195 (mp0) cc_final: 0.7740 (mp0) REVERT: A 543 TRP cc_start: 0.3447 (t60) cc_final: 0.3008 (t60) REVERT: A 561 ARG cc_start: 0.8473 (ptt180) cc_final: 0.8018 (mmt180) REVERT: A 588 ARG cc_start: 0.7730 (mmt90) cc_final: 0.7402 (tmt170) REVERT: A 624 ASP cc_start: 0.7622 (m-30) cc_final: 0.7149 (p0) REVERT: A 629 MET cc_start: 0.7171 (ppp) cc_final: 0.6851 (ppp) REVERT: A 631 ARG cc_start: 0.8346 (ttt180) cc_final: 0.7461 (ttm-80) REVERT: A 673 VAL cc_start: 0.9208 (p) cc_final: 0.8951 (p) REVERT: A 714 VAL cc_start: 0.8946 (t) cc_final: 0.8666 (p) REVERT: A 749 PHE cc_start: 0.7441 (m-10) cc_final: 0.6930 (m-10) REVERT: A 776 GLN cc_start: 0.8933 (mt0) cc_final: 0.8563 (tp40) REVERT: A 802 LEU cc_start: 0.5871 (pp) cc_final: 0.5364 (mt) REVERT: A 808 TYR cc_start: 0.6825 (t80) cc_final: 0.6266 (t80) REVERT: B 170 GLU cc_start: 0.8781 (tt0) cc_final: 0.8519 (tp30) REVERT: B 283 MET cc_start: 0.8303 (tpp) cc_final: 0.7983 (tmm) REVERT: B 403 MET cc_start: 0.7780 (mmt) cc_final: 0.7391 (mmm) REVERT: B 430 MET cc_start: 0.2675 (mmm) cc_final: 0.2021 (ttm) REVERT: B 629 MET cc_start: 0.8558 (ppp) cc_final: 0.7998 (ppp) REVERT: B 632 ILE cc_start: 0.8912 (mt) cc_final: 0.8659 (mp) REVERT: B 633 ASP cc_start: 0.8609 (p0) cc_final: 0.7560 (p0) REVERT: B 719 ASN cc_start: 0.8499 (p0) cc_final: 0.7771 (m110) REVERT: B 758 ASP cc_start: 0.8434 (t0) cc_final: 0.7464 (m-30) REVERT: B 759 GLU cc_start: 0.8018 (tt0) cc_final: 0.7426 (tt0) REVERT: B 782 LEU cc_start: 0.9455 (tp) cc_final: 0.9185 (tp) REVERT: B 846 LEU cc_start: 0.9480 (mt) cc_final: 0.9257 (tp) REVERT: C 177 LEU cc_start: 0.8998 (tp) cc_final: 0.8648 (tp) REVERT: C 186 GLU cc_start: 0.8004 (mp0) cc_final: 0.7801 (mp0) REVERT: C 196 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.8034 (mtm-85) REVERT: C 232 LEU cc_start: 0.8897 (mt) cc_final: 0.8654 (mt) REVERT: C 257 GLU cc_start: 0.8789 (tt0) cc_final: 0.8140 (tm-30) REVERT: C 274 ILE cc_start: 0.9370 (mp) cc_final: 0.9130 (tt) REVERT: C 498 MET cc_start: 0.4994 (mmm) cc_final: 0.4696 (mmm) REVERT: C 581 SER cc_start: 0.8420 (m) cc_final: 0.8216 (p) REVERT: C 595 ASN cc_start: 0.8524 (m-40) cc_final: 0.7701 (p0) REVERT: C 615 CYS cc_start: 0.9329 (m) cc_final: 0.8832 (t) REVERT: C 627 GLU cc_start: 0.6952 (mp0) cc_final: 0.6665 (tm-30) REVERT: C 633 ASP cc_start: 0.7546 (t0) cc_final: 0.7283 (t0) REVERT: C 716 MET cc_start: 0.8172 (mtp) cc_final: 0.7496 (ttm) REVERT: C 821 ILE cc_start: 0.8241 (mt) cc_final: 0.7631 (mt) REVERT: C 827 ASN cc_start: 0.9351 (m-40) cc_final: 0.9079 (m-40) REVERT: D 204 LEU cc_start: 0.9288 (mm) cc_final: 0.9049 (mm) REVERT: D 358 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7518 (mm-30) REVERT: D 396 GLU cc_start: 0.9037 (tp30) cc_final: 0.8420 (tp30) REVERT: D 524 MET cc_start: 0.5186 (mmm) cc_final: 0.4520 (mmt) REVERT: D 691 LEU cc_start: 0.8114 (mt) cc_final: 0.7715 (mt) REVERT: E 195 GLN cc_start: 0.8009 (pt0) cc_final: 0.7391 (mm-40) REVERT: E 217 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7123 (tt0) REVERT: E 254 GLU cc_start: 0.7267 (mp0) cc_final: 0.6987 (mt-10) REVERT: E 319 TYR cc_start: 0.8746 (t80) cc_final: 0.8490 (t80) REVERT: E 443 MET cc_start: 0.5636 (tmm) cc_final: 0.3801 (mtt) REVERT: E 475 ILE cc_start: 0.7809 (pt) cc_final: 0.7490 (pt) REVERT: E 562 MET cc_start: 0.7976 (tpp) cc_final: 0.7492 (tpt) REVERT: E 638 MET cc_start: 0.8221 (pmm) cc_final: 0.7815 (ptm) REVERT: E 642 SER cc_start: 0.8618 (m) cc_final: 0.7401 (p) REVERT: E 687 PHE cc_start: 0.8394 (m-10) cc_final: 0.7920 (m-80) REVERT: E 756 ARG cc_start: 0.8196 (ptp-110) cc_final: 0.7723 (ptt90) REVERT: E 817 LEU cc_start: 0.9276 (tp) cc_final: 0.9021 (tp) REVERT: F 298 MET cc_start: 0.5888 (mmm) cc_final: 0.5483 (mmm) REVERT: F 319 TYR cc_start: 0.8018 (t80) cc_final: 0.7535 (t80) REVERT: F 324 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6430 (tp30) REVERT: F 498 MET cc_start: 0.6266 (tpp) cc_final: 0.5896 (tpp) REVERT: F 512 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6266 (mt0) REVERT: F 613 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8371 (tt0) REVERT: F 614 LEU cc_start: 0.8648 (tp) cc_final: 0.8369 (mt) REVERT: F 716 MET cc_start: 0.9259 (mpp) cc_final: 0.8901 (mpp) REVERT: F 737 MET cc_start: 0.7939 (mmm) cc_final: 0.7712 (tpp) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.4177 time to fit residues: 382.1902 Evaluate side-chains 399 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 268 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 309 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 568 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN E 794 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN F 688 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33285 Z= 0.245 Angle : 0.682 15.480 44929 Z= 0.339 Chirality : 0.044 0.277 5088 Planarity : 0.004 0.051 5869 Dihedral : 8.816 144.045 4748 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 4077 helix: 1.00 (0.11), residues: 2320 sheet: -1.91 (0.25), residues: 386 loop : -1.59 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 543 HIS 0.006 0.001 HIS A 360 PHE 0.023 0.002 PHE F 763 TYR 0.019 0.001 TYR F 656 ARG 0.013 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8475 (m-40) cc_final: 0.8150 (m-40) REVERT: A 241 ASP cc_start: 0.8382 (t0) cc_final: 0.8129 (t0) REVERT: A 242 MET cc_start: 0.7924 (mmm) cc_final: 0.7241 (mmm) REVERT: A 293 MET cc_start: 0.3287 (tpp) cc_final: 0.2651 (mmt) REVERT: A 459 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 561 ARG cc_start: 0.8485 (ptt180) cc_final: 0.8028 (mmt180) REVERT: A 588 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7540 (tmt170) REVERT: A 624 ASP cc_start: 0.7629 (m-30) cc_final: 0.7138 (p0) REVERT: A 631 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7386 (ttm-80) REVERT: A 714 VAL cc_start: 0.9025 (t) cc_final: 0.8710 (p) REVERT: A 717 THR cc_start: 0.8429 (p) cc_final: 0.8210 (p) REVERT: A 749 PHE cc_start: 0.7523 (m-10) cc_final: 0.7062 (m-10) REVERT: A 776 GLN cc_start: 0.8930 (mt0) cc_final: 0.8552 (tp40) REVERT: A 802 LEU cc_start: 0.5732 (pp) cc_final: 0.5339 (mt) REVERT: B 170 GLU cc_start: 0.8800 (tt0) cc_final: 0.8549 (tp30) REVERT: B 186 GLU cc_start: 0.8307 (mp0) cc_final: 0.7785 (mp0) REVERT: B 283 MET cc_start: 0.8481 (tpp) cc_final: 0.8165 (tmm) REVERT: B 293 MET cc_start: 0.7110 (tpp) cc_final: 0.6720 (tpt) REVERT: B 310 CYS cc_start: 0.7980 (t) cc_final: 0.7616 (t) REVERT: B 333 PHE cc_start: 0.9099 (m-80) cc_final: 0.8781 (m-10) REVERT: B 403 MET cc_start: 0.7884 (mmt) cc_final: 0.7509 (mmm) REVERT: B 430 MET cc_start: 0.2543 (mmm) cc_final: 0.1868 (ttm) REVERT: B 629 MET cc_start: 0.8759 (ppp) cc_final: 0.8017 (ppp) REVERT: B 719 ASN cc_start: 0.8508 (p0) cc_final: 0.7873 (m110) REVERT: B 737 MET cc_start: 0.7117 (mmt) cc_final: 0.6752 (mmt) REVERT: B 758 ASP cc_start: 0.8261 (t0) cc_final: 0.7475 (m-30) REVERT: B 759 GLU cc_start: 0.8139 (tt0) cc_final: 0.7476 (tt0) REVERT: B 846 LEU cc_start: 0.9471 (mt) cc_final: 0.9251 (tp) REVERT: C 177 LEU cc_start: 0.8969 (tp) cc_final: 0.8605 (tp) REVERT: C 185 GLU cc_start: 0.8871 (pm20) cc_final: 0.8669 (pm20) REVERT: C 196 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8003 (mtm-85) REVERT: C 232 LEU cc_start: 0.8928 (mt) cc_final: 0.8670 (mt) REVERT: C 257 GLU cc_start: 0.8915 (tt0) cc_final: 0.8253 (tm-30) REVERT: C 524 MET cc_start: 0.0978 (ttt) cc_final: 0.0529 (ttp) REVERT: C 595 ASN cc_start: 0.8528 (m-40) cc_final: 0.7741 (p0) REVERT: C 615 CYS cc_start: 0.9333 (m) cc_final: 0.8796 (t) REVERT: C 633 ASP cc_start: 0.7547 (t0) cc_final: 0.7272 (t0) REVERT: C 827 ASN cc_start: 0.9384 (m-40) cc_final: 0.9007 (t0) REVERT: D 204 LEU cc_start: 0.9329 (mm) cc_final: 0.9064 (mm) REVERT: D 358 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7509 (mm-30) REVERT: D 396 GLU cc_start: 0.9032 (tp30) cc_final: 0.8364 (tp30) REVERT: D 524 MET cc_start: 0.5224 (mmm) cc_final: 0.4659 (mmt) REVERT: D 691 LEU cc_start: 0.8207 (mt) cc_final: 0.7793 (mt) REVERT: E 195 GLN cc_start: 0.8077 (pt0) cc_final: 0.7448 (mm-40) REVERT: E 217 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7226 (tt0) REVERT: E 254 GLU cc_start: 0.7310 (mp0) cc_final: 0.7043 (mt-10) REVERT: E 318 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8632 (mm-30) REVERT: E 319 TYR cc_start: 0.8689 (t80) cc_final: 0.8478 (t80) REVERT: E 350 LEU cc_start: 0.9053 (mm) cc_final: 0.8738 (tp) REVERT: E 443 MET cc_start: 0.5588 (tmm) cc_final: 0.3741 (mtt) REVERT: E 475 ILE cc_start: 0.7818 (pt) cc_final: 0.7491 (pt) REVERT: E 562 MET cc_start: 0.7956 (tpp) cc_final: 0.7498 (tpt) REVERT: E 638 MET cc_start: 0.8308 (pmm) cc_final: 0.7832 (ptm) REVERT: E 642 SER cc_start: 0.8684 (m) cc_final: 0.7526 (t) REVERT: E 687 PHE cc_start: 0.8440 (m-10) cc_final: 0.7981 (m-80) REVERT: E 853 ILE cc_start: 0.8977 (tt) cc_final: 0.8708 (mm) REVERT: F 240 LEU cc_start: 0.7294 (tp) cc_final: 0.6710 (tt) REVERT: F 319 TYR cc_start: 0.8253 (t80) cc_final: 0.7736 (t80) REVERT: F 324 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6383 (tp30) REVERT: F 498 MET cc_start: 0.6276 (tpp) cc_final: 0.5917 (tpp) REVERT: F 512 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6316 (mt0) REVERT: F 613 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8461 (tt0) REVERT: F 614 LEU cc_start: 0.8637 (tp) cc_final: 0.8348 (mt) REVERT: F 716 MET cc_start: 0.9251 (mpp) cc_final: 0.8905 (mpp) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.4116 time to fit residues: 357.4472 Evaluate side-chains 396 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 7.9990 chunk 347 optimal weight: 0.0270 chunk 366 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN F 688 ASN F 711 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33285 Z= 0.279 Angle : 0.711 16.759 44929 Z= 0.353 Chirality : 0.044 0.217 5088 Planarity : 0.005 0.048 5869 Dihedral : 8.890 143.654 4748 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 4077 helix: 0.90 (0.11), residues: 2303 sheet: -2.02 (0.24), residues: 404 loop : -1.56 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 543 HIS 0.007 0.001 HIS A 360 PHE 0.025 0.002 PHE F 621 TYR 0.029 0.002 TYR F 322 ARG 0.011 0.001 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 4.119 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 201 ASN cc_start: 0.8382 (m-40) cc_final: 0.7830 (m110) REVERT: A 241 ASP cc_start: 0.8485 (t0) cc_final: 0.8252 (t0) REVERT: A 242 MET cc_start: 0.7949 (mmm) cc_final: 0.7326 (mmm) REVERT: A 293 MET cc_start: 0.3320 (tpp) cc_final: 0.2701 (mmt) REVERT: A 310 CYS cc_start: 0.8029 (t) cc_final: 0.7828 (t) REVERT: A 318 GLU cc_start: 0.8199 (mp0) cc_final: 0.7827 (mp0) REVERT: A 459 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8188 (mm-30) REVERT: A 561 ARG cc_start: 0.8506 (ptt180) cc_final: 0.8024 (mmt180) REVERT: A 624 ASP cc_start: 0.8157 (m-30) cc_final: 0.7685 (p0) REVERT: A 631 ARG cc_start: 0.8392 (ttt180) cc_final: 0.7429 (ttm-80) REVERT: A 714 VAL cc_start: 0.9080 (t) cc_final: 0.8733 (p) REVERT: A 749 PHE cc_start: 0.7504 (m-10) cc_final: 0.7074 (m-10) REVERT: A 776 GLN cc_start: 0.8926 (mt0) cc_final: 0.8517 (tp40) REVERT: B 170 GLU cc_start: 0.8793 (tt0) cc_final: 0.8561 (tp30) REVERT: B 186 GLU cc_start: 0.8290 (mp0) cc_final: 0.7689 (mp0) REVERT: B 310 CYS cc_start: 0.8043 (t) cc_final: 0.7692 (t) REVERT: B 333 PHE cc_start: 0.9206 (m-80) cc_final: 0.8828 (m-10) REVERT: B 430 MET cc_start: 0.2625 (mmm) cc_final: 0.2050 (ttm) REVERT: B 536 ILE cc_start: 0.9203 (mt) cc_final: 0.8925 (tp) REVERT: B 629 MET cc_start: 0.8852 (ppp) cc_final: 0.8029 (ppp) REVERT: B 633 ASP cc_start: 0.8492 (p0) cc_final: 0.8287 (p0) REVERT: B 719 ASN cc_start: 0.8531 (p0) cc_final: 0.7852 (m110) REVERT: B 737 MET cc_start: 0.7137 (mmt) cc_final: 0.6723 (mmt) REVERT: B 758 ASP cc_start: 0.8488 (t0) cc_final: 0.7630 (m-30) REVERT: B 759 GLU cc_start: 0.8131 (tt0) cc_final: 0.7485 (tt0) REVERT: C 177 LEU cc_start: 0.8951 (tp) cc_final: 0.8543 (tp) REVERT: C 257 GLU cc_start: 0.8984 (tt0) cc_final: 0.8661 (tp30) REVERT: C 524 MET cc_start: 0.1304 (ttt) cc_final: 0.0868 (ttp) REVERT: C 595 ASN cc_start: 0.8557 (m-40) cc_final: 0.7921 (p0) REVERT: C 615 CYS cc_start: 0.9352 (m) cc_final: 0.8822 (t) REVERT: C 633 ASP cc_start: 0.7635 (t0) cc_final: 0.7382 (t0) REVERT: C 739 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8204 (tm-30) REVERT: C 827 ASN cc_start: 0.9357 (m-40) cc_final: 0.9019 (t0) REVERT: D 204 LEU cc_start: 0.9320 (mm) cc_final: 0.9109 (mm) REVERT: D 358 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7474 (mm-30) REVERT: D 396 GLU cc_start: 0.9021 (tp30) cc_final: 0.8452 (tp30) REVERT: D 524 MET cc_start: 0.5114 (mmm) cc_final: 0.4475 (mmt) REVERT: D 691 LEU cc_start: 0.7937 (mt) cc_final: 0.7528 (mt) REVERT: E 195 GLN cc_start: 0.8154 (pt0) cc_final: 0.7511 (mm-40) REVERT: E 254 GLU cc_start: 0.7326 (mp0) cc_final: 0.7066 (mt-10) REVERT: E 278 ASP cc_start: 0.7506 (p0) cc_final: 0.6813 (t0) REVERT: E 318 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8674 (mm-30) REVERT: E 443 MET cc_start: 0.5632 (tmm) cc_final: 0.3800 (mtm) REVERT: E 475 ILE cc_start: 0.7841 (pt) cc_final: 0.7515 (pt) REVERT: E 552 MET cc_start: 0.6889 (pmm) cc_final: 0.6654 (pmm) REVERT: E 562 MET cc_start: 0.8006 (tpp) cc_final: 0.7619 (tpp) REVERT: E 564 GLN cc_start: 0.7604 (tt0) cc_final: 0.7226 (mp10) REVERT: E 638 MET cc_start: 0.8449 (pmm) cc_final: 0.7959 (ptp) REVERT: E 642 SER cc_start: 0.8711 (m) cc_final: 0.7699 (p) REVERT: E 739 GLU cc_start: 0.8555 (tp30) cc_final: 0.7819 (pp20) REVERT: E 762 VAL cc_start: 0.9239 (t) cc_final: 0.8919 (p) REVERT: E 853 ILE cc_start: 0.9018 (tt) cc_final: 0.8744 (mm) REVERT: F 240 LEU cc_start: 0.7294 (tp) cc_final: 0.6693 (tt) REVERT: F 319 TYR cc_start: 0.8221 (t80) cc_final: 0.7774 (t80) REVERT: F 324 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6480 (tp30) REVERT: F 498 MET cc_start: 0.6292 (tpp) cc_final: 0.5946 (tpp) REVERT: F 512 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6252 (mt0) REVERT: F 613 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8462 (tt0) REVERT: F 614 LEU cc_start: 0.8723 (tp) cc_final: 0.8369 (mt) REVERT: F 644 SER cc_start: 0.4529 (p) cc_final: 0.4162 (t) REVERT: F 716 MET cc_start: 0.9231 (mpp) cc_final: 0.8902 (mpp) REVERT: F 737 MET cc_start: 0.7979 (mmm) cc_final: 0.7610 (mmm) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.4217 time to fit residues: 363.8217 Evaluate side-chains 383 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 407 optimal weight: 50.0000 chunk 375 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 0.0020 chunk 198 optimal weight: 9.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 HIS ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33285 Z= 0.251 Angle : 0.702 17.469 44929 Z= 0.348 Chirality : 0.044 0.222 5088 Planarity : 0.005 0.078 5869 Dihedral : 8.871 141.179 4748 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.37 (0.13), residues: 4077 helix: 0.85 (0.11), residues: 2330 sheet: -2.01 (0.24), residues: 404 loop : -1.53 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 543 HIS 0.007 0.001 HIS C 641 PHE 0.025 0.002 PHE F 621 TYR 0.017 0.001 TYR F 656 ARG 0.022 0.001 ARG E 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8423 (m-40) cc_final: 0.7832 (m-40) REVERT: A 241 ASP cc_start: 0.8568 (t0) cc_final: 0.8333 (t0) REVERT: A 242 MET cc_start: 0.7939 (mmm) cc_final: 0.7462 (mmm) REVERT: A 293 MET cc_start: 0.3275 (tpp) cc_final: 0.2691 (mmt) REVERT: A 318 GLU cc_start: 0.8297 (mp0) cc_final: 0.7834 (mp0) REVERT: A 459 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 561 ARG cc_start: 0.8541 (ptt180) cc_final: 0.8063 (mmt180) REVERT: A 624 ASP cc_start: 0.8159 (m-30) cc_final: 0.7709 (p0) REVERT: A 631 ARG cc_start: 0.8349 (ttt180) cc_final: 0.7436 (ttm-80) REVERT: A 714 VAL cc_start: 0.9107 (t) cc_final: 0.8758 (p) REVERT: A 749 PHE cc_start: 0.7517 (m-10) cc_final: 0.7115 (m-10) REVERT: A 776 GLN cc_start: 0.8936 (mt0) cc_final: 0.8525 (tp40) REVERT: B 186 GLU cc_start: 0.8194 (mp0) cc_final: 0.7970 (mp0) REVERT: B 310 CYS cc_start: 0.8081 (t) cc_final: 0.7759 (t) REVERT: B 333 PHE cc_start: 0.9145 (m-80) cc_final: 0.8848 (m-10) REVERT: B 430 MET cc_start: 0.2704 (mmm) cc_final: 0.2124 (ttm) REVERT: B 536 ILE cc_start: 0.9230 (mt) cc_final: 0.8960 (tp) REVERT: B 629 MET cc_start: 0.8865 (ppp) cc_final: 0.8030 (ppp) REVERT: B 719 ASN cc_start: 0.8421 (p0) cc_final: 0.7807 (m110) REVERT: B 737 MET cc_start: 0.7033 (mmt) cc_final: 0.6640 (mmt) REVERT: B 758 ASP cc_start: 0.8499 (t0) cc_final: 0.7707 (m-30) REVERT: C 177 LEU cc_start: 0.8942 (tp) cc_final: 0.8541 (tp) REVERT: C 257 GLU cc_start: 0.8981 (tt0) cc_final: 0.8485 (tp30) REVERT: C 524 MET cc_start: 0.1203 (ttt) cc_final: 0.0943 (ttt) REVERT: C 595 ASN cc_start: 0.8503 (m-40) cc_final: 0.7920 (p0) REVERT: C 615 CYS cc_start: 0.9306 (m) cc_final: 0.8781 (t) REVERT: C 739 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 827 ASN cc_start: 0.9275 (m-40) cc_final: 0.8986 (m-40) REVERT: D 204 LEU cc_start: 0.9302 (mm) cc_final: 0.9081 (mm) REVERT: D 358 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7442 (mm-30) REVERT: D 524 MET cc_start: 0.5138 (mmm) cc_final: 0.4519 (mmt) REVERT: D 642 SER cc_start: 0.9409 (m) cc_final: 0.8886 (t) REVERT: D 663 THR cc_start: 0.9733 (p) cc_final: 0.9238 (t) REVERT: D 691 LEU cc_start: 0.7900 (mt) cc_final: 0.7519 (mt) REVERT: E 195 GLN cc_start: 0.7914 (pt0) cc_final: 0.7499 (mm-40) REVERT: E 254 GLU cc_start: 0.7346 (mp0) cc_final: 0.7086 (mt-10) REVERT: E 278 ASP cc_start: 0.7702 (p0) cc_final: 0.7086 (t0) REVERT: E 443 MET cc_start: 0.5709 (tmm) cc_final: 0.3895 (mtm) REVERT: E 475 ILE cc_start: 0.7914 (pt) cc_final: 0.7573 (pt) REVERT: E 552 MET cc_start: 0.7172 (pmm) cc_final: 0.6743 (pmm) REVERT: E 562 MET cc_start: 0.7899 (tpp) cc_final: 0.7434 (tpp) REVERT: E 564 GLN cc_start: 0.7536 (tt0) cc_final: 0.7249 (mp10) REVERT: E 638 MET cc_start: 0.8498 (pmm) cc_final: 0.8197 (ptp) REVERT: E 642 SER cc_start: 0.8760 (m) cc_final: 0.7703 (p) REVERT: E 739 GLU cc_start: 0.8570 (tp30) cc_final: 0.7806 (pp20) REVERT: E 762 VAL cc_start: 0.9299 (t) cc_final: 0.8974 (p) REVERT: E 853 ILE cc_start: 0.9027 (tt) cc_final: 0.8765 (mm) REVERT: F 167 ASP cc_start: 0.7386 (t0) cc_final: 0.6811 (t0) REVERT: F 240 LEU cc_start: 0.7349 (tp) cc_final: 0.6712 (tt) REVERT: F 319 TYR cc_start: 0.8116 (t80) cc_final: 0.7637 (t80) REVERT: F 324 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6635 (tp30) REVERT: F 498 MET cc_start: 0.6424 (tpp) cc_final: 0.6092 (tpp) REVERT: F 614 LEU cc_start: 0.8792 (tp) cc_final: 0.8533 (mt) REVERT: F 644 SER cc_start: 0.4417 (p) cc_final: 0.4022 (t) REVERT: F 716 MET cc_start: 0.9223 (mpp) cc_final: 0.8884 (mpp) REVERT: F 737 MET cc_start: 0.7980 (mmm) cc_final: 0.7671 (mmm) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.4108 time to fit residues: 357.1324 Evaluate side-chains 382 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.119725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.097233 restraints weight = 113183.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.096788 restraints weight = 82558.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097762 restraints weight = 68082.999| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33285 Z= 0.257 Angle : 0.700 17.686 44929 Z= 0.347 Chirality : 0.044 0.183 5088 Planarity : 0.004 0.065 5869 Dihedral : 8.872 140.032 4748 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.34 (0.13), residues: 4077 helix: 0.88 (0.11), residues: 2325 sheet: -2.02 (0.24), residues: 405 loop : -1.53 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 543 HIS 0.007 0.001 HIS A 360 PHE 0.026 0.002 PHE F 621 TYR 0.018 0.001 TYR D 656 ARG 0.015 0.001 ARG E 756 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7718.31 seconds wall clock time: 140 minutes 30.25 seconds (8430.25 seconds total)