Starting phenix.real_space_refine on Fri Mar 22 09:01:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/03_2024/6rn3_4941_updated.pdb" } resolution = 4.0 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= 0.009 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 31 5.49 5 S 127 5.16 5 C 20485 2.51 5 N 5933 2.21 5 O 6295 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 ARG 550": "NH1" <-> "NH2" Residue "A TYR 653": "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 "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32871 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" 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: "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': 2, 'PTRANS': 22, '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': 2, 'PTRANS': 22, 'TRANS': 659} Chain breaks: 3 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: 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: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" 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} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.03, per 1000 atoms: 0.55 Number of scatterers: 32871 At special positions: 0 Unit cell: (144.56, 182, 166.4, 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 127 16.00 P 31 15.00 O 6295 8.00 N 5933 7.00 C 20485 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: 13.17 Conformation dependent library (CDL) restraints added in 6.2 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 24 sheets defined 55.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.596A pdb=" N LEU A 245 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA A 247 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 248 " --> pdb=" O LEU A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' 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 359 removed outlier: 4.830A pdb=" N LEU A 359 " --> pdb=" O GLU A 355 " (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: 4.007A 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 543 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 668 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 696 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 734 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 805 Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'B' and resid 161 through 164 No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 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 254 through 266 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 295 through 303 Proline residue: B 301 - end of helix 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 360 Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 388 through 405 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 444 through 492 Processing helix chain 'B' and resid 496 through 523 Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 611 through 622 removed outlier: 3.590A pdb=" N CYS B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 647 removed outlier: 4.044A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 4.402A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 654 through 658' Processing helix chain 'B' and resid 662 through 668 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 720 through 728 removed outlier: 4.407A pdb=" N ASP B 723 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 724 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 725 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 728 " --> pdb=" O ILE B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 748 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 834 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 213 through 225 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 248 removed outlier: 3.691A pdb=" N ALA C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 269 removed outlier: 4.004A pdb=" N GLN C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 343 through 361 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: 4.269A 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 543 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 640 through 646 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 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 768 through 789 Processing helix chain 'C' and resid 797 through 807 Processing helix chain 'C' and resid 815 through 833 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 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 284 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.683A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.592A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.936A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) 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 411 through 429 Processing helix chain 'D' and resid 444 through 492 Processing helix chain 'D' and resid 495 through 523 removed outlier: 3.980A 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 566 Processing helix chain 'D' and resid 574 through 589 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 640 through 643 Processing helix chain 'D' and resid 656 through 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' 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 684 through 696 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 734 through 748 Processing helix chain 'D' and resid 751 through 756 removed outlier: 3.515A pdb=" N ARG D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 815 through 833 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' 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 243 through 248 removed outlier: 4.309A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (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 300 through 305 removed outlier: 4.501A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 300 through 305' Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 327 through 329 No H-bonds generated for 'chain 'E' and resid 327 through 329' Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.055A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 405 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 541 Processing helix chain 'E' and resid 553 through 560 Processing helix chain 'E' and resid 562 through 569 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 612 through 622 Processing helix chain 'E' and resid 642 through 646 Processing helix chain 'E' and resid 654 through 656 No H-bonds generated for 'chain 'E' and resid 654 through 656' Processing helix chain 'E' and resid 662 through 665 No H-bonds generated for 'chain 'E' and resid 662 through 665' 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 685 through 696 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 756 removed outlier: 3.850A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 789 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 835 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 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.926A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 410 through 429 Processing helix chain 'F' and resid 444 through 492 Processing helix chain 'F' and resid 495 through 523 removed outlier: 3.990A 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 568 Processing helix chain 'F' and resid 574 through 587 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 679 through 681 No H-bonds generated for 'chain 'F' and resid 679 through 681' Processing helix chain 'F' and resid 684 through 695 Processing helix chain 'F' and resid 721 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 815 through 835 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 334 through 337 removed outlier: 6.491A pdb=" N GLY A 312 " --> pdb=" O LEU A 204 " (cutoff:3.500A) 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 600 through 603 removed outlier: 7.103A pdb=" N VAL A 714 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 603 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 717 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 792 through 795 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 311 through 314 removed outlier: 7.725A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.845A 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 759 through 761 removed outlier: 3.954A pdb=" N VAL B 714 " --> pdb=" O GLY B 599 " (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 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 334 through 337 removed outlier: 6.708A pdb=" N GLY C 312 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 599 through 603 removed outlier: 6.514A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 793 through 795 removed outlier: 6.030A 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 removed outlier: 5.300A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 630 through 633 Processing sheet with id= P, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.587A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.547A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 240 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL E 311 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 206 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 601 through 603 removed outlier: 6.218A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.619A pdb=" N VAL E 707 " --> pdb=" O LEU E 699 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 793 through 795 removed outlier: 5.954A pdb=" N ILE E 844 " --> pdb=" O HIS E 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 165 through 167 Processing sheet with id= V, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.784A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.805A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 604 " --> pdb=" O VAL F 761 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 792 through 795 removed outlier: 3.809A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1604 hydrogen bonds defined for protein. 4770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 14.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11712 1.36 - 1.51: 9837 1.51 - 1.66: 11539 1.66 - 1.80: 211 1.80 - 1.95: 22 Bond restraints: 33321 Sorted by residual: bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.528 1.427 0.101 2.61e-02 1.47e+03 1.51e+01 bond pdb=" C ALA E 814 " pdb=" N ARG E 815 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.09e-02 8.42e+03 9.48e+00 bond pdb=" CG ARG E 815 " pdb=" CD ARG E 815 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.81e+00 bond pdb=" CA SER D 600 " pdb=" CB SER D 600 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" CA ALA B 628 " pdb=" CB ALA B 628 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.51e-02 4.39e+03 7.23e+00 ... (remaining 33316 not shown) Histogram of bond angle deviations from ideal: 96.42 - 106.74: 1063 106.74 - 117.06: 22723 117.06 - 127.38: 20917 127.38 - 137.70: 264 137.70 - 148.02: 3 Bond angle restraints: 44970 Sorted by residual: angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CA PRO B 409 " ideal model delta sigma weight residual 127.00 148.02 -21.02 2.40e+00 1.74e-01 7.67e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CA PRO E 409 " ideal model delta sigma weight residual 127.00 147.50 -20.50 2.40e+00 1.74e-01 7.30e+01 angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 120.60 103.18 17.42 2.20e+00 2.07e-01 6.27e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CD PRO E 409 " ideal model delta sigma weight residual 120.60 103.33 17.27 2.20e+00 2.07e-01 6.16e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 113.50 106.47 7.03 1.23e+00 6.61e-01 3.26e+01 ... (remaining 44965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 20149 26.42 - 52.85: 453 52.85 - 79.27: 50 79.27 - 105.70: 5 105.70 - 132.12: 2 Dihedral angle restraints: 20659 sinusoidal: 8775 harmonic: 11884 Sorted by residual: dihedral pdb=" CA GLU C 207 " pdb=" C GLU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA HIS E 568 " pdb=" C HIS E 568 " pdb=" N ARG E 569 " pdb=" CA ARG E 569 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA LEU F 245 " pdb=" C LEU F 245 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " ideal model delta harmonic sigma weight residual -180.00 -147.73 -32.27 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 20656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3464 0.057 - 0.114: 1286 0.114 - 0.172: 294 0.172 - 0.229: 41 0.229 - 0.286: 8 Chirality restraints: 5093 Sorted by residual: 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 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 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 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG D 815 " pdb=" N ARG D 815 " pdb=" C ARG D 815 " pdb=" CB ARG D 815 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5090 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.056 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.026 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 301 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 683 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 684 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " 0.043 5.00e-02 4.00e+02 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3709 2.74 - 3.28: 31749 3.28 - 3.82: 54243 3.82 - 4.36: 63534 4.36 - 4.90: 107187 Nonbonded interactions: 260422 Sorted by model distance: nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.198 2.440 nonbonded pdb=" O1B AGS E1002 " pdb=" O2A AGS E1002 " model vdw 2.199 2.440 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.220 2.440 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.232 2.440 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.235 2.440 ... (remaining 260417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'F' and resid 159 through 858) } 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: 0.760 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: 5.570 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 86.410 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.010 0.109 33321 Z= 0.685 Angle : 1.151 21.024 44970 Z= 0.615 Chirality : 0.061 0.286 5093 Planarity : 0.008 0.086 5872 Dihedral : 11.261 132.121 12979 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 0.35 % Allowed : 0.90 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % 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: -3.79 (0.11), residues: 4053 helix: -2.10 (0.08), residues: 2310 sheet: -3.11 (0.23), residues: 374 loop : -2.76 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP D 543 HIS 0.018 0.003 HIS A 362 PHE 0.046 0.004 PHE C 763 TYR 0.028 0.003 TYR F 671 ARG 0.017 0.001 ARG E 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1138 time to evaluate : 3.444 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: A 163 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7701 (mtpp) REVERT: A 180 VAL cc_start: 0.6759 (t) cc_final: 0.6077 (m) REVERT: A 181 ILE cc_start: 0.8080 (mt) cc_final: 0.7869 (mp) REVERT: A 241 ASP cc_start: 0.7032 (t0) cc_final: 0.6746 (t0) REVERT: A 322 TYR cc_start: 0.8094 (m-80) cc_final: 0.7881 (m-80) REVERT: A 363 VAL cc_start: 0.6968 (m) cc_final: 0.6190 (m) REVERT: A 430 MET cc_start: -0.1309 (mmm) cc_final: -0.1609 (mtm) REVERT: A 616 LYS cc_start: 0.7333 (mttt) cc_final: 0.6997 (mttt) REVERT: A 740 LEU cc_start: 0.7619 (tp) cc_final: 0.7311 (pp) REVERT: A 804 SER cc_start: 0.5371 (t) cc_final: 0.5082 (p) REVERT: B 194 LEU cc_start: 0.8817 (mt) cc_final: 0.8568 (mp) REVERT: B 457 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8459 (tm-30) REVERT: B 524 MET cc_start: 0.1090 (mmm) cc_final: -0.0487 (ptt) REVERT: B 533 ASP cc_start: 0.8393 (p0) cc_final: 0.8109 (p0) REVERT: B 562 MET cc_start: 0.6919 (tmt) cc_final: 0.5971 (ttp) REVERT: B 633 ASP cc_start: 0.8186 (m-30) cc_final: 0.7354 (m-30) REVERT: B 634 MET cc_start: 0.7932 (mmm) cc_final: 0.7462 (tpp) REVERT: B 685 ASP cc_start: 0.7333 (p0) cc_final: 0.6816 (p0) REVERT: B 693 VAL cc_start: 0.8838 (t) cc_final: 0.8614 (t) REVERT: B 736 HIS cc_start: 0.8142 (m170) cc_final: 0.7704 (m90) REVERT: B 747 HIS cc_start: 0.7110 (m-70) cc_final: 0.6821 (m90) REVERT: B 802 LEU cc_start: 0.8343 (mp) cc_final: 0.8086 (pp) REVERT: C 178 ASP cc_start: 0.7721 (m-30) cc_final: 0.7404 (p0) REVERT: C 200 ASN cc_start: 0.8927 (m-40) cc_final: 0.7961 (p0) REVERT: C 217 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 259 LEU cc_start: 0.7925 (tp) cc_final: 0.6728 (tp) REVERT: C 314 THR cc_start: 0.8978 (t) cc_final: 0.8729 (p) REVERT: C 345 ASP cc_start: 0.8007 (m-30) cc_final: 0.7204 (t0) REVERT: C 410 GLU cc_start: 0.3172 (mp0) cc_final: 0.2574 (tt0) REVERT: C 656 TYR cc_start: 0.7566 (t80) cc_final: 0.7024 (t80) REVERT: C 696 ASP cc_start: 0.7786 (m-30) cc_final: 0.7475 (m-30) REVERT: C 747 HIS cc_start: 0.8027 (m-70) cc_final: 0.7813 (m-70) REVERT: C 791 TYR cc_start: 0.7319 (m-80) cc_final: 0.6323 (m-10) REVERT: D 187 ILE cc_start: 0.7700 (mt) cc_final: 0.7491 (mt) REVERT: D 293 MET cc_start: 0.3836 (tpt) cc_final: 0.3553 (tpp) REVERT: D 319 TYR cc_start: 0.8737 (t80) cc_final: 0.8164 (t80) REVERT: D 430 MET cc_start: 0.2930 (mmm) cc_final: 0.1872 (ppp) REVERT: D 562 MET cc_start: 0.8153 (tpt) cc_final: 0.7911 (tpt) REVERT: D 630 VAL cc_start: 0.8412 (t) cc_final: 0.8140 (t) REVERT: D 680 GLU cc_start: 0.8065 (pm20) cc_final: 0.7436 (pp20) REVERT: D 689 ILE cc_start: 0.8038 (mm) cc_final: 0.7292 (mm) REVERT: D 780 LYS cc_start: 0.8726 (mttt) cc_final: 0.8194 (tmmt) REVERT: D 808 TYR cc_start: 0.6799 (t80) cc_final: 0.6402 (t80) REVERT: D 827 ASN cc_start: 0.8791 (m-40) cc_final: 0.8484 (m110) REVERT: E 185 GLU cc_start: 0.8328 (tt0) cc_final: 0.7955 (tp30) REVERT: E 187 ILE cc_start: 0.7993 (mt) cc_final: 0.7785 (mt) REVERT: E 395 ASP cc_start: 0.7577 (t0) cc_final: 0.7350 (t0) REVERT: E 551 MET cc_start: 0.6682 (mmp) cc_final: 0.6323 (mtm) REVERT: E 739 GLU cc_start: 0.8263 (tp30) cc_final: 0.7686 (pt0) REVERT: E 783 TYR cc_start: 0.7344 (m-10) cc_final: 0.6917 (m-10) REVERT: E 784 LYS cc_start: 0.9032 (tttt) cc_final: 0.8829 (ptpt) REVERT: F 245 LEU cc_start: 0.8758 (mt) cc_final: 0.8232 (mp) REVERT: F 582 ASN cc_start: 0.8539 (m-40) cc_final: 0.8230 (t0) REVERT: F 673 VAL cc_start: 0.7253 (t) cc_final: 0.6954 (m) REVERT: F 680 GLU cc_start: 0.6386 (pm20) cc_final: 0.6160 (pm20) REVERT: F 686 VAL cc_start: 0.7984 (t) cc_final: 0.7481 (t) REVERT: F 766 LEU cc_start: 0.7586 (pt) cc_final: 0.6739 (mp) REVERT: F 779 LEU cc_start: 0.7997 (mm) cc_final: 0.7555 (tp) REVERT: F 795 ILE cc_start: 0.7435 (tt) cc_final: 0.7151 (tt) REVERT: F 796 SER cc_start: 0.8671 (t) cc_final: 0.8328 (p) REVERT: F 817 LEU cc_start: 0.8942 (tp) cc_final: 0.8535 (tp) REVERT: F 821 ILE cc_start: 0.8586 (mt) cc_final: 0.8104 (mt) outliers start: 12 outliers final: 0 residues processed: 1149 average time/residue: 0.5011 time to fit residues: 872.1546 Evaluate side-chains 614 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 3.725 ------------------------------------------------------------------------------- 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: 5.9990 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 320 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 371 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 361 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS A 827 ASN A 849 ASN A 858 HIS B 195 GLN B 281 HIS B 334 GLN B 620 ASN ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN D 195 GLN D 281 HIS D 567 HIS D 595 ASN D 692 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 281 HIS E 309 HIS ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 567 HIS E 641 HIS E 755 ASN E 823 GLN E 857 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 361 HIS F 512 GLN F 688 ASN F 770 HIS ** F 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 849 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33321 Z= 0.241 Angle : 0.718 9.250 44970 Z= 0.366 Chirality : 0.045 0.272 5093 Planarity : 0.005 0.073 5872 Dihedral : 9.556 116.492 4741 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 3.00 % Allowed : 11.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 4053 helix: -0.45 (0.10), residues: 2296 sheet: -2.58 (0.24), residues: 414 loop : -2.24 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 543 HIS 0.020 0.001 HIS A 747 PHE 0.019 0.002 PHE B 729 TYR 0.022 0.002 TYR F 671 ARG 0.008 0.001 ARG F 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 680 time to evaluate : 3.666 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: A 166 ILE cc_start: 0.8389 (mp) cc_final: 0.8179 (pt) REVERT: A 242 MET cc_start: 0.7959 (mmt) cc_final: 0.7522 (mmt) REVERT: A 481 GLN cc_start: 0.6714 (pt0) cc_final: 0.6212 (tt0) REVERT: A 519 LEU cc_start: 0.8256 (tp) cc_final: 0.7994 (mt) REVERT: A 623 PHE cc_start: 0.7241 (t80) cc_final: 0.6583 (t80) REVERT: A 661 TYR cc_start: 0.7253 (t80) cc_final: 0.6981 (t80) REVERT: A 692 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: B 335 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7688 (tttt) REVERT: B 358 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7283 (pt0) REVERT: B 457 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8456 (tm-30) REVERT: B 524 MET cc_start: 0.0988 (mmm) cc_final: -0.0444 (ptt) REVERT: B 535 GLU cc_start: 0.7809 (mp0) cc_final: 0.7549 (mp0) REVERT: B 633 ASP cc_start: 0.7946 (m-30) cc_final: 0.6773 (m-30) REVERT: B 634 MET cc_start: 0.8023 (mmm) cc_final: 0.7723 (tpp) REVERT: B 685 ASP cc_start: 0.7370 (p0) cc_final: 0.6841 (p0) REVERT: B 736 HIS cc_start: 0.7854 (m170) cc_final: 0.7652 (m90) REVERT: B 747 HIS cc_start: 0.7165 (m-70) cc_final: 0.6815 (m90) REVERT: B 819 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7872 (mtm110) REVERT: C 217 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7763 (mt-10) REVERT: C 345 ASP cc_start: 0.7843 (m-30) cc_final: 0.7133 (t0) REVERT: C 385 GLN cc_start: 0.8109 (mm-40) cc_final: 0.6968 (mm-40) REVERT: C 410 GLU cc_start: 0.3155 (mp0) cc_final: 0.2746 (tt0) REVERT: C 524 MET cc_start: 0.4556 (tpp) cc_final: 0.4330 (tpp) REVERT: C 656 TYR cc_start: 0.7949 (t80) cc_final: 0.7648 (t80) REVERT: C 696 ASP cc_start: 0.7832 (m-30) cc_final: 0.7540 (m-30) REVERT: C 700 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7742 (p) REVERT: D 293 MET cc_start: 0.4108 (tpt) cc_final: 0.3541 (tpt) REVERT: D 430 MET cc_start: 0.2827 (mmm) cc_final: 0.1819 (ppp) REVERT: D 552 MET cc_start: 0.7274 (ppp) cc_final: 0.6600 (ppp) REVERT: D 614 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9108 (tt) REVERT: D 633 ASP cc_start: 0.8042 (m-30) cc_final: 0.7613 (m-30) REVERT: D 642 SER cc_start: 0.9044 (m) cc_final: 0.8732 (t) REVERT: D 692 GLN cc_start: 0.7740 (tt0) cc_final: 0.7511 (tt0) REVERT: D 780 LYS cc_start: 0.8654 (mttt) cc_final: 0.8286 (tmmt) REVERT: D 827 ASN cc_start: 0.8921 (m-40) cc_final: 0.8445 (m110) REVERT: E 185 GLU cc_start: 0.8289 (tt0) cc_final: 0.7982 (tp30) REVERT: E 230 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6501 (mm-30) REVERT: E 233 LYS cc_start: 0.7626 (mttm) cc_final: 0.7368 (mmtt) REVERT: E 329 LEU cc_start: 0.8099 (mt) cc_final: 0.7769 (pp) REVERT: E 737 MET cc_start: 0.7412 (tpp) cc_final: 0.6760 (tpp) REVERT: E 739 GLU cc_start: 0.8177 (tp30) cc_final: 0.7611 (pt0) REVERT: E 740 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7731 (pp) REVERT: F 188 ARG cc_start: 0.7377 (ttm110) cc_final: 0.6932 (tpp80) REVERT: F 282 THR cc_start: 0.7704 (m) cc_final: 0.7137 (m) REVERT: F 297 ASN cc_start: 0.6855 (m110) cc_final: 0.6290 (m-40) REVERT: F 329 LEU cc_start: 0.8206 (tp) cc_final: 0.7978 (tt) REVERT: F 403 MET cc_start: 0.8592 (mmp) cc_final: 0.7633 (mtm) REVERT: F 460 GLU cc_start: 0.8561 (pp20) cc_final: 0.8114 (pp20) REVERT: F 466 LYS cc_start: 0.7327 (mtpt) cc_final: 0.7097 (mmtt) REVERT: F 498 MET cc_start: 0.6496 (tpp) cc_final: 0.5742 (mmm) REVERT: F 538 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7761 (tp30) REVERT: F 582 ASN cc_start: 0.8590 (m-40) cc_final: 0.8136 (t0) REVERT: F 766 LEU cc_start: 0.7322 (pt) cc_final: 0.6739 (mp) REVERT: F 779 LEU cc_start: 0.8007 (mm) cc_final: 0.7655 (tp) REVERT: F 817 LEU cc_start: 0.8962 (tp) cc_final: 0.8621 (tp) REVERT: F 821 ILE cc_start: 0.8372 (mt) cc_final: 0.8008 (mt) outliers start: 103 outliers final: 54 residues processed: 745 average time/residue: 0.4407 time to fit residues: 528.1991 Evaluate side-chains 609 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 551 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 804 SER Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 0.0470 chunk 115 optimal weight: 0.8980 chunk 309 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 401 optimal weight: 0.8980 chunk 331 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 512 GLN B 620 ASN B 641 HIS B 711 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 748 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 823 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 473 GLN F 831 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33321 Z= 0.207 Angle : 0.674 17.544 44970 Z= 0.336 Chirality : 0.043 0.185 5093 Planarity : 0.005 0.066 5872 Dihedral : 8.975 147.999 4741 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.11 % Allowed : 13.82 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4053 helix: 0.37 (0.11), residues: 2271 sheet: -2.24 (0.24), residues: 420 loop : -1.97 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 462 HIS 0.007 0.001 HIS F 281 PHE 0.017 0.002 PHE F 255 TYR 0.035 0.002 TYR B 783 ARG 0.007 0.000 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 580 time to evaluate : 3.529 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: A 166 ILE cc_start: 0.8395 (mp) cc_final: 0.8156 (pt) REVERT: A 242 MET cc_start: 0.8023 (mmt) cc_final: 0.7811 (mmt) REVERT: A 298 MET cc_start: 0.8017 (mmm) cc_final: 0.7749 (tpt) REVERT: A 481 GLN cc_start: 0.6557 (pt0) cc_final: 0.5957 (tt0) REVERT: A 519 LEU cc_start: 0.8094 (tp) cc_final: 0.7860 (mt) REVERT: A 528 ARG cc_start: 0.7178 (mmt90) cc_final: 0.6929 (mmt90) REVERT: A 661 TYR cc_start: 0.7438 (t80) cc_final: 0.7155 (t80) REVERT: A 812 TYR cc_start: 0.6075 (t80) cc_final: 0.5841 (t80) REVERT: B 358 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7203 (pt0) REVERT: B 457 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8441 (tm-30) REVERT: B 535 GLU cc_start: 0.7799 (mp0) cc_final: 0.7558 (mp0) REVERT: B 634 MET cc_start: 0.8064 (mmm) cc_final: 0.7764 (tpp) REVERT: B 685 ASP cc_start: 0.7560 (p0) cc_final: 0.7033 (p0) REVERT: B 708 ASP cc_start: 0.8181 (t0) cc_final: 0.7484 (p0) REVERT: B 747 HIS cc_start: 0.7199 (m-70) cc_final: 0.6895 (m-70) REVERT: B 819 ARG cc_start: 0.8166 (ptt-90) cc_final: 0.7753 (mtm110) REVERT: C 293 MET cc_start: 0.7947 (tpp) cc_final: 0.7146 (tmm) REVERT: C 345 ASP cc_start: 0.7785 (m-30) cc_final: 0.7115 (t0) REVERT: C 385 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7915 (mm-40) REVERT: C 396 GLU cc_start: 0.8156 (tt0) cc_final: 0.7743 (tp30) REVERT: C 410 GLU cc_start: 0.3213 (mp0) cc_final: 0.2889 (tt0) REVERT: C 696 ASP cc_start: 0.7968 (m-30) cc_final: 0.7604 (m-30) REVERT: C 700 THR cc_start: 0.8170 (m) cc_final: 0.7704 (p) REVERT: D 230 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7581 (tm-30) REVERT: D 252 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.5890 (ttt180) REVERT: D 260 LYS cc_start: 0.7148 (mmmt) cc_final: 0.6761 (ptmm) REVERT: D 298 MET cc_start: 0.7041 (mtm) cc_final: 0.6800 (mtm) REVERT: D 430 MET cc_start: 0.2554 (mmm) cc_final: 0.1779 (ppp) REVERT: D 614 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9187 (tt) REVERT: D 636 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7162 (mt-10) REVERT: D 677 ASP cc_start: 0.7894 (t0) cc_final: 0.7643 (t0) REVERT: D 780 LYS cc_start: 0.8719 (mttt) cc_final: 0.8262 (tmmt) REVERT: D 827 ASN cc_start: 0.8887 (m-40) cc_final: 0.8376 (m110) REVERT: D 846 LEU cc_start: 0.9421 (mt) cc_final: 0.9206 (mt) REVERT: E 185 GLU cc_start: 0.8339 (tt0) cc_final: 0.7982 (tp30) REVERT: E 230 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6665 (mm-30) REVERT: E 318 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7830 (mm-30) REVERT: E 329 LEU cc_start: 0.8114 (mt) cc_final: 0.7670 (pp) REVERT: E 460 GLU cc_start: 0.8536 (tp30) cc_final: 0.8018 (mm-30) REVERT: E 533 ASP cc_start: 0.8096 (t0) cc_final: 0.7608 (m-30) REVERT: E 681 LYS cc_start: 0.7905 (mptt) cc_final: 0.7005 (mmtt) REVERT: E 685 ASP cc_start: 0.6761 (p0) cc_final: 0.6342 (p0) REVERT: E 739 GLU cc_start: 0.8179 (tp30) cc_final: 0.7919 (tp30) REVERT: E 821 ILE cc_start: 0.8420 (mt) cc_final: 0.8174 (mp) REVERT: F 242 MET cc_start: 0.7362 (mtt) cc_final: 0.7029 (mtt) REVERT: F 329 LEU cc_start: 0.8187 (tp) cc_final: 0.7882 (tt) REVERT: F 466 LYS cc_start: 0.7040 (mtpt) cc_final: 0.6779 (mmtt) REVERT: F 538 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7735 (tp30) REVERT: F 582 ASN cc_start: 0.8553 (m-40) cc_final: 0.7991 (t0) REVERT: F 766 LEU cc_start: 0.7268 (pt) cc_final: 0.6689 (mp) REVERT: F 779 LEU cc_start: 0.7979 (mm) cc_final: 0.7661 (tp) REVERT: F 821 ILE cc_start: 0.8472 (mt) cc_final: 0.8239 (mt) REVERT: F 850 GLU cc_start: 0.6195 (pm20) cc_final: 0.5398 (tt0) outliers start: 107 outliers final: 61 residues processed: 643 average time/residue: 0.4250 time to fit residues: 448.0282 Evaluate side-chains 553 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 490 time to evaluate : 4.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 723 ASP Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 373 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 454 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 823 GLN F 269 GLN F 688 ASN F 849 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33321 Z= 0.211 Angle : 0.629 9.622 44970 Z= 0.315 Chirality : 0.042 0.178 5093 Planarity : 0.004 0.052 5872 Dihedral : 8.644 151.918 4741 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.64 % Allowed : 14.78 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4053 helix: 0.76 (0.11), residues: 2287 sheet: -2.07 (0.25), residues: 438 loop : -1.78 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 462 HIS 0.007 0.001 HIS B 641 PHE 0.018 0.002 PHE A 749 TYR 0.049 0.002 TYR B 783 ARG 0.007 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 529 time to evaluate : 3.630 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: A 228 VAL cc_start: 0.9425 (p) cc_final: 0.9137 (m) REVERT: A 298 MET cc_start: 0.8118 (mmm) cc_final: 0.7767 (tpt) REVERT: A 329 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8919 (tp) REVERT: A 481 GLN cc_start: 0.6646 (pt0) cc_final: 0.6014 (tt0) REVERT: A 519 LEU cc_start: 0.8081 (tp) cc_final: 0.7848 (mt) REVERT: A 528 ARG cc_start: 0.7215 (mmt90) cc_final: 0.6703 (tpp-160) REVERT: A 562 MET cc_start: 0.7480 (mtp) cc_final: 0.7240 (mmm) REVERT: A 601 PHE cc_start: 0.8452 (m-80) cc_final: 0.8066 (m-80) REVERT: A 642 SER cc_start: 0.8043 (m) cc_final: 0.7448 (t) REVERT: A 661 TYR cc_start: 0.7622 (t80) cc_final: 0.7299 (t80) REVERT: B 186 GLU cc_start: 0.8101 (mp0) cc_final: 0.7771 (mp0) REVERT: B 242 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7311 (mmm) REVERT: B 358 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7324 (pt0) REVERT: B 359 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 457 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8465 (tm-30) REVERT: B 524 MET cc_start: 0.1330 (mmt) cc_final: -0.0606 (ptt) REVERT: B 562 MET cc_start: 0.6083 (tmt) cc_final: 0.4965 (tmm) REVERT: B 633 ASP cc_start: 0.7801 (m-30) cc_final: 0.7594 (m-30) REVERT: B 685 ASP cc_start: 0.7637 (p0) cc_final: 0.7146 (p0) REVERT: B 700 THR cc_start: 0.8462 (m) cc_final: 0.7843 (p) REVERT: B 708 ASP cc_start: 0.8146 (t0) cc_final: 0.7483 (p0) REVERT: B 747 HIS cc_start: 0.7204 (m-70) cc_final: 0.6804 (m170) REVERT: B 793 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 260 LYS cc_start: 0.8829 (tttt) cc_final: 0.8306 (tptt) REVERT: C 280 LEU cc_start: 0.9034 (tp) cc_final: 0.8684 (tp) REVERT: C 293 MET cc_start: 0.8181 (tpp) cc_final: 0.7266 (tmm) REVERT: C 345 ASP cc_start: 0.7754 (m-30) cc_final: 0.7073 (t0) REVERT: C 385 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7955 (mm-40) REVERT: C 410 GLU cc_start: 0.3195 (mp0) cc_final: 0.2801 (tt0) REVERT: C 696 ASP cc_start: 0.8014 (m-30) cc_final: 0.7691 (m-30) REVERT: C 700 THR cc_start: 0.8346 (m) cc_final: 0.7894 (p) REVERT: D 210 VAL cc_start: 0.8975 (m) cc_final: 0.8767 (m) REVERT: D 252 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.5966 (ttt180) REVERT: D 260 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6907 (ptmm) REVERT: D 377 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8216 (p) REVERT: D 430 MET cc_start: 0.2378 (mmm) cc_final: 0.1697 (ppp) REVERT: D 614 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9227 (tt) REVERT: D 636 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7346 (mt-10) REVERT: D 677 ASP cc_start: 0.7839 (t0) cc_final: 0.7634 (t0) REVERT: D 780 LYS cc_start: 0.8710 (mttt) cc_final: 0.8334 (tmtt) REVERT: D 826 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 827 ASN cc_start: 0.8906 (m-40) cc_final: 0.8333 (m110) REVERT: E 185 GLU cc_start: 0.8386 (tt0) cc_final: 0.7889 (tp30) REVERT: E 230 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6652 (mm-30) REVERT: E 298 MET cc_start: 0.7042 (mtm) cc_final: 0.6425 (pmm) REVERT: E 318 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 322 TYR cc_start: 0.6974 (m-10) cc_final: 0.6465 (m-80) REVERT: E 329 LEU cc_start: 0.7983 (mt) cc_final: 0.7534 (pp) REVERT: E 396 GLU cc_start: 0.8838 (tt0) cc_final: 0.8581 (tp30) REVERT: E 460 GLU cc_start: 0.8494 (tp30) cc_final: 0.7995 (mm-30) REVERT: E 739 GLU cc_start: 0.8238 (tp30) cc_final: 0.8007 (tp30) REVERT: E 747 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7365 (t-90) REVERT: F 329 LEU cc_start: 0.8224 (tp) cc_final: 0.7947 (tt) REVERT: F 403 MET cc_start: 0.8605 (mmp) cc_final: 0.7739 (mtm) REVERT: F 466 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6749 (mmtt) REVERT: F 538 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7754 (tp30) REVERT: F 661 TYR cc_start: 0.6246 (m-80) cc_final: 0.5998 (m-80) REVERT: F 779 LEU cc_start: 0.8055 (mm) cc_final: 0.7726 (tp) REVERT: F 821 ILE cc_start: 0.8417 (mt) cc_final: 0.8177 (mt) REVERT: F 850 GLU cc_start: 0.6118 (pm20) cc_final: 0.5307 (tt0) outliers start: 125 outliers final: 78 residues processed: 603 average time/residue: 0.4228 time to fit residues: 418.1320 Evaluate side-chains 558 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 472 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 354 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN B 620 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 822 GLN D 200 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 849 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 831 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33321 Z= 0.240 Angle : 0.631 8.697 44970 Z= 0.317 Chirality : 0.043 0.270 5093 Planarity : 0.004 0.050 5872 Dihedral : 8.552 160.539 4741 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.87 % Allowed : 15.51 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 4053 helix: 0.93 (0.11), residues: 2295 sheet: -2.01 (0.25), residues: 437 loop : -1.65 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 543 HIS 0.011 0.001 HIS A 281 PHE 0.029 0.002 PHE C 729 TYR 0.066 0.002 TYR B 783 ARG 0.011 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 489 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9098 (tp) REVERT: A 392 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8002 (t0) REVERT: A 481 GLN cc_start: 0.6581 (pt0) cc_final: 0.6075 (tt0) REVERT: A 528 ARG cc_start: 0.7247 (mmt90) cc_final: 0.6723 (tpp-160) REVERT: A 601 PHE cc_start: 0.8666 (m-80) cc_final: 0.8301 (m-80) REVERT: A 661 TYR cc_start: 0.7760 (t80) cc_final: 0.7474 (t80) REVERT: A 812 TYR cc_start: 0.6227 (t80) cc_final: 0.5919 (t80) REVERT: B 358 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7280 (pt0) REVERT: B 457 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8455 (tm-30) REVERT: B 524 MET cc_start: 0.1417 (mmt) cc_final: -0.0518 (ptt) REVERT: B 685 ASP cc_start: 0.7773 (p0) cc_final: 0.7278 (p0) REVERT: B 700 THR cc_start: 0.8627 (m) cc_final: 0.8020 (p) REVERT: B 747 HIS cc_start: 0.7271 (m-70) cc_final: 0.6773 (m170) REVERT: B 843 VAL cc_start: 0.8034 (t) cc_final: 0.7705 (p) REVERT: C 181 ILE cc_start: 0.9202 (mp) cc_final: 0.8905 (mt) REVERT: C 260 LYS cc_start: 0.8777 (tttt) cc_final: 0.8428 (tptt) REVERT: C 280 LEU cc_start: 0.9105 (tp) cc_final: 0.8800 (tp) REVERT: C 293 MET cc_start: 0.8214 (tpp) cc_final: 0.7256 (tmm) REVERT: C 405 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 410 GLU cc_start: 0.3292 (mp0) cc_final: 0.2795 (tt0) REVERT: C 562 MET cc_start: 0.9004 (tpt) cc_final: 0.8777 (tpt) REVERT: C 615 CYS cc_start: 0.8941 (m) cc_final: 0.8699 (m) REVERT: C 696 ASP cc_start: 0.7961 (m-30) cc_final: 0.7676 (m-30) REVERT: C 700 THR cc_start: 0.8543 (m) cc_final: 0.8188 (p) REVERT: C 716 MET cc_start: 0.7782 (mtm) cc_final: 0.7573 (mtp) REVERT: D 252 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6109 (ttt180) REVERT: D 396 GLU cc_start: 0.8739 (tt0) cc_final: 0.8527 (tt0) REVERT: D 430 MET cc_start: 0.2409 (mmm) cc_final: 0.1698 (ppp) REVERT: D 636 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7272 (mt-10) REVERT: D 640 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8017 (ttpp) REVERT: D 677 ASP cc_start: 0.7920 (t0) cc_final: 0.7635 (t0) REVERT: D 780 LYS cc_start: 0.8793 (mttt) cc_final: 0.8407 (tmtt) REVERT: D 826 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7990 (mt-10) REVERT: D 827 ASN cc_start: 0.8961 (m-40) cc_final: 0.8330 (m110) REVERT: E 185 GLU cc_start: 0.8294 (tt0) cc_final: 0.7796 (tp30) REVERT: E 230 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6674 (mm-30) REVERT: E 298 MET cc_start: 0.7083 (mtm) cc_final: 0.6474 (pmm) REVERT: E 318 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 322 TYR cc_start: 0.7063 (m-80) cc_final: 0.6530 (m-80) REVERT: E 396 GLU cc_start: 0.8814 (tt0) cc_final: 0.8551 (tp30) REVERT: E 460 GLU cc_start: 0.8508 (tp30) cc_final: 0.8014 (mm-30) REVERT: E 543 TRP cc_start: 0.8426 (t-100) cc_final: 0.8221 (m-90) REVERT: E 739 GLU cc_start: 0.8311 (tp30) cc_final: 0.8071 (tp30) REVERT: E 747 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7388 (t-90) REVERT: E 821 ILE cc_start: 0.8562 (mp) cc_final: 0.8311 (mp) REVERT: F 403 MET cc_start: 0.8606 (mmp) cc_final: 0.7804 (mtm) REVERT: F 538 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7732 (tp30) REVERT: F 604 LEU cc_start: 0.8250 (mt) cc_final: 0.8034 (mt) REVERT: F 821 ILE cc_start: 0.8448 (mt) cc_final: 0.8178 (mt) REVERT: F 850 GLU cc_start: 0.6091 (pm20) cc_final: 0.5257 (tt0) outliers start: 133 outliers final: 87 residues processed: 577 average time/residue: 0.4019 time to fit residues: 387.3128 Evaluate side-chains 542 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 450 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 0.9980 chunk 356 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 395 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 711 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 573 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 269 GLN D 321 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 GLN F 831 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 33321 Z= 0.297 Angle : 0.676 8.878 44970 Z= 0.340 Chirality : 0.044 0.214 5093 Planarity : 0.005 0.052 5872 Dihedral : 8.478 163.076 4741 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.84 % Allowed : 16.73 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 4053 helix: 0.88 (0.11), residues: 2310 sheet: -2.05 (0.24), residues: 439 loop : -1.69 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 543 HIS 0.009 0.001 HIS C 764 PHE 0.025 0.002 PHE C 729 TYR 0.047 0.002 TYR B 783 ARG 0.009 0.001 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 493 time to evaluate : 3.910 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: A 265 ASP cc_start: 0.7860 (m-30) cc_final: 0.7554 (t70) REVERT: A 392 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8130 (t0) REVERT: A 481 GLN cc_start: 0.6634 (pt0) cc_final: 0.6099 (tt0) REVERT: A 562 MET cc_start: 0.7426 (mmm) cc_final: 0.7049 (mmm) REVERT: A 601 PHE cc_start: 0.8737 (m-80) cc_final: 0.8367 (m-80) REVERT: A 661 TYR cc_start: 0.7967 (t80) cc_final: 0.7730 (t80) REVERT: B 242 MET cc_start: 0.8298 (mmm) cc_final: 0.8070 (mmm) REVERT: B 293 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6665 (mtt) REVERT: B 358 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7302 (pt0) REVERT: B 457 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8342 (tm-30) REVERT: B 524 MET cc_start: 0.1538 (mmt) cc_final: -0.0376 (ptt) REVERT: B 535 GLU cc_start: 0.7766 (mp0) cc_final: 0.7553 (mp0) REVERT: B 685 ASP cc_start: 0.7888 (p0) cc_final: 0.7377 (p0) REVERT: B 700 THR cc_start: 0.8790 (m) cc_final: 0.8236 (p) REVERT: B 747 HIS cc_start: 0.7349 (m-70) cc_final: 0.6904 (m-70) REVERT: C 181 ILE cc_start: 0.9205 (mp) cc_final: 0.9001 (mt) REVERT: C 217 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 260 LYS cc_start: 0.9016 (tttt) cc_final: 0.8627 (tptt) REVERT: C 280 LEU cc_start: 0.9181 (tp) cc_final: 0.8955 (tt) REVERT: C 405 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8248 (mt) REVERT: C 410 GLU cc_start: 0.3334 (mp0) cc_final: 0.2521 (tt0) REVERT: C 524 MET cc_start: 0.4369 (tpp) cc_final: 0.3999 (tpp) REVERT: C 540 LEU cc_start: 0.9014 (tp) cc_final: 0.8798 (tp) REVERT: C 696 ASP cc_start: 0.8014 (m-30) cc_final: 0.7759 (m-30) REVERT: C 700 THR cc_start: 0.8708 (m) cc_final: 0.8251 (p) REVERT: C 716 MET cc_start: 0.7980 (mtm) cc_final: 0.7704 (mtp) REVERT: C 812 TYR cc_start: 0.8108 (m-80) cc_final: 0.7730 (m-10) REVERT: D 184 ASP cc_start: 0.7364 (p0) cc_final: 0.7130 (p0) REVERT: D 252 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6059 (ttt180) REVERT: D 260 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6903 (tttm) REVERT: D 627 GLU cc_start: 0.7050 (pm20) cc_final: 0.6512 (pp20) REVERT: D 636 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 640 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8097 (ttpp) REVERT: D 677 ASP cc_start: 0.7926 (t0) cc_final: 0.7651 (t0) REVERT: D 691 LEU cc_start: 0.8563 (tp) cc_final: 0.8141 (tp) REVERT: D 780 LYS cc_start: 0.8911 (mttt) cc_final: 0.8584 (tmtt) REVERT: D 826 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8117 (mt-10) REVERT: E 185 GLU cc_start: 0.8101 (tt0) cc_final: 0.7569 (tp30) REVERT: E 188 ARG cc_start: 0.7468 (ttm110) cc_final: 0.6736 (tpt90) REVERT: E 278 ASP cc_start: 0.8875 (p0) cc_final: 0.8656 (p0) REVERT: E 318 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 319 TYR cc_start: 0.8239 (t80) cc_final: 0.7917 (t80) REVERT: E 330 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6921 (tp30) REVERT: E 460 GLU cc_start: 0.8531 (tp30) cc_final: 0.8077 (mm-30) REVERT: E 543 TRP cc_start: 0.8481 (t-100) cc_final: 0.7898 (m-90) REVERT: E 739 GLU cc_start: 0.8355 (tp30) cc_final: 0.8069 (tp30) REVERT: E 747 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7536 (t-90) REVERT: F 207 GLU cc_start: 0.7113 (mp0) cc_final: 0.6747 (mp0) REVERT: F 299 LEU cc_start: 0.8061 (mp) cc_final: 0.7526 (pp) REVERT: F 661 TYR cc_start: 0.6597 (m-80) cc_final: 0.6185 (m-80) outliers start: 132 outliers final: 99 residues processed: 585 average time/residue: 0.4209 time to fit residues: 406.8547 Evaluate side-chains 542 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 438 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 394 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN D 692 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33321 Z= 0.200 Angle : 0.618 15.404 44970 Z= 0.312 Chirality : 0.043 0.197 5093 Planarity : 0.004 0.056 5872 Dihedral : 8.372 176.168 4741 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.14 % Allowed : 18.60 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 4053 helix: 1.02 (0.11), residues: 2318 sheet: -1.93 (0.25), residues: 437 loop : -1.59 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 462 HIS 0.010 0.001 HIS F 281 PHE 0.029 0.002 PHE C 729 TYR 0.047 0.001 TYR B 783 ARG 0.010 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 483 time to evaluate : 4.157 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: A 265 ASP cc_start: 0.7777 (m-30) cc_final: 0.7495 (t70) REVERT: A 326 ASP cc_start: 0.8580 (t0) cc_final: 0.8330 (t0) REVERT: A 392 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 481 GLN cc_start: 0.6657 (pt0) cc_final: 0.6212 (tt0) REVERT: A 601 PHE cc_start: 0.8745 (m-80) cc_final: 0.8416 (m-80) REVERT: A 661 TYR cc_start: 0.7935 (t80) cc_final: 0.7604 (t80) REVERT: A 812 TYR cc_start: 0.5878 (t80) cc_final: 0.5605 (t80) REVERT: A 823 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: B 358 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7065 (pt0) REVERT: B 457 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8442 (tm-30) REVERT: B 524 MET cc_start: 0.1614 (mmt) cc_final: -0.0115 (ptt) REVERT: B 535 GLU cc_start: 0.7723 (mp0) cc_final: 0.7482 (mp0) REVERT: B 685 ASP cc_start: 0.7832 (p0) cc_final: 0.7322 (p0) REVERT: B 700 THR cc_start: 0.8727 (m) cc_final: 0.8193 (p) REVERT: B 747 HIS cc_start: 0.7307 (m-70) cc_final: 0.6834 (m170) REVERT: B 843 VAL cc_start: 0.8255 (t) cc_final: 0.7945 (p) REVERT: C 181 ILE cc_start: 0.9143 (mp) cc_final: 0.8940 (mt) REVERT: C 217 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 242 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7874 (mtt) REVERT: C 254 GLU cc_start: 0.8824 (tp30) cc_final: 0.8544 (tp30) REVERT: C 260 LYS cc_start: 0.8981 (tttt) cc_final: 0.8560 (tptt) REVERT: C 293 MET cc_start: 0.8374 (mmm) cc_final: 0.7403 (tmm) REVERT: C 410 GLU cc_start: 0.3497 (mp0) cc_final: 0.2706 (tt0) REVERT: C 562 MET cc_start: 0.9092 (tpt) cc_final: 0.8482 (tpt) REVERT: C 700 THR cc_start: 0.8686 (m) cc_final: 0.8317 (p) REVERT: C 716 MET cc_start: 0.7911 (mtm) cc_final: 0.7659 (mtp) REVERT: C 812 TYR cc_start: 0.7929 (m-80) cc_final: 0.7551 (m-10) REVERT: D 173 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7911 (tt0) REVERT: D 184 ASP cc_start: 0.7265 (p0) cc_final: 0.6951 (p0) REVERT: D 252 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6050 (ttt180) REVERT: D 260 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6802 (tttm) REVERT: D 636 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7080 (mt-10) REVERT: D 640 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8169 (ttpp) REVERT: D 677 ASP cc_start: 0.7942 (t0) cc_final: 0.7636 (t0) REVERT: D 780 LYS cc_start: 0.8902 (mttt) cc_final: 0.8549 (tmtt) REVERT: E 184 ASP cc_start: 0.8237 (t0) cc_final: 0.8018 (t0) REVERT: E 185 GLU cc_start: 0.8047 (tt0) cc_final: 0.7578 (tp30) REVERT: E 278 ASP cc_start: 0.8872 (p0) cc_final: 0.8647 (p0) REVERT: E 318 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 330 GLU cc_start: 0.7524 (tm-30) cc_final: 0.6895 (tp30) REVERT: E 396 GLU cc_start: 0.8767 (tt0) cc_final: 0.8143 (tp30) REVERT: E 460 GLU cc_start: 0.8483 (tp30) cc_final: 0.8065 (mm-30) REVERT: E 543 TRP cc_start: 0.8629 (t-100) cc_final: 0.8220 (m-90) REVERT: E 681 LYS cc_start: 0.7824 (mptt) cc_final: 0.7486 (mmtt) REVERT: E 739 GLU cc_start: 0.8284 (tp30) cc_final: 0.8066 (tp30) REVERT: E 747 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7390 (t-90) REVERT: E 821 ILE cc_start: 0.8696 (mp) cc_final: 0.8447 (mp) REVERT: F 207 GLU cc_start: 0.7171 (mp0) cc_final: 0.6784 (mp0) REVERT: F 224 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7816 (tp) REVERT: F 359 LEU cc_start: 0.8503 (pp) cc_final: 0.7783 (mm) REVERT: F 466 LYS cc_start: 0.6997 (tttt) cc_final: 0.6642 (mptt) REVERT: F 498 MET cc_start: 0.6457 (tpp) cc_final: 0.5345 (mmm) REVERT: F 661 TYR cc_start: 0.6622 (m-10) cc_final: 0.6147 (m-80) REVERT: F 801 LYS cc_start: 0.8943 (pttp) cc_final: 0.8525 (mmtt) REVERT: F 850 GLU cc_start: 0.5990 (pm20) cc_final: 0.5265 (tt0) outliers start: 108 outliers final: 80 residues processed: 549 average time/residue: 0.4107 time to fit residues: 377.3292 Evaluate side-chains 532 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 446 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 640 LYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 309 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 778 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33321 Z= 0.170 Angle : 0.608 11.894 44970 Z= 0.301 Chirality : 0.042 0.364 5093 Planarity : 0.004 0.049 5872 Dihedral : 8.203 169.157 4741 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.32 % Allowed : 18.98 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 4053 helix: 1.16 (0.11), residues: 2305 sheet: -1.81 (0.25), residues: 442 loop : -1.54 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 462 HIS 0.008 0.001 HIS F 281 PHE 0.032 0.002 PHE C 729 TYR 0.043 0.001 TYR B 783 ARG 0.009 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 476 time to evaluate : 3.626 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: A 265 ASP cc_start: 0.7819 (m-30) cc_final: 0.7529 (t70) REVERT: A 326 ASP cc_start: 0.8571 (t0) cc_final: 0.8337 (t0) REVERT: A 392 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 481 GLN cc_start: 0.6718 (pt0) cc_final: 0.6263 (tt0) REVERT: A 661 TYR cc_start: 0.7955 (t80) cc_final: 0.7647 (t80) REVERT: A 812 TYR cc_start: 0.6009 (t80) cc_final: 0.5762 (t80) REVERT: B 358 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7258 (pt0) REVERT: B 457 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8455 (tm-30) REVERT: B 524 MET cc_start: 0.1588 (mmt) cc_final: -0.0046 (ptt) REVERT: B 535 GLU cc_start: 0.7709 (mp0) cc_final: 0.7484 (mp0) REVERT: B 668 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7471 (mmt180) REVERT: B 685 ASP cc_start: 0.7832 (p0) cc_final: 0.7306 (p0) REVERT: B 700 THR cc_start: 0.8693 (m) cc_final: 0.8203 (p) REVERT: B 747 HIS cc_start: 0.7372 (m-70) cc_final: 0.6794 (m170) REVERT: B 843 VAL cc_start: 0.8306 (t) cc_final: 0.7999 (p) REVERT: C 181 ILE cc_start: 0.9060 (mp) cc_final: 0.8789 (mt) REVERT: C 217 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7815 (mt-10) REVERT: C 242 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: C 254 GLU cc_start: 0.8832 (tp30) cc_final: 0.8564 (tp30) REVERT: C 260 LYS cc_start: 0.9006 (tttt) cc_final: 0.8602 (tptt) REVERT: C 350 LEU cc_start: 0.9253 (mt) cc_final: 0.9036 (mt) REVERT: C 396 GLU cc_start: 0.8543 (tt0) cc_final: 0.7988 (tm-30) REVERT: C 405 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 410 GLU cc_start: 0.3609 (mp0) cc_final: 0.2792 (tt0) REVERT: C 700 THR cc_start: 0.8697 (m) cc_final: 0.8343 (p) REVERT: C 716 MET cc_start: 0.7893 (mtm) cc_final: 0.7673 (mtp) REVERT: D 184 ASP cc_start: 0.7289 (p0) cc_final: 0.6946 (p0) REVERT: D 252 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6136 (ttt180) REVERT: D 260 LYS cc_start: 0.7363 (mmmt) cc_final: 0.6836 (tttm) REVERT: D 640 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8123 (ttpp) REVERT: D 647 VAL cc_start: 0.9220 (p) cc_final: 0.8930 (t) REVERT: D 677 ASP cc_start: 0.7840 (t0) cc_final: 0.7476 (t0) REVERT: D 780 LYS cc_start: 0.8867 (mttt) cc_final: 0.8505 (tmtt) REVERT: E 185 GLU cc_start: 0.8078 (tt0) cc_final: 0.7569 (tp30) REVERT: E 278 ASP cc_start: 0.8831 (p0) cc_final: 0.8611 (p0) REVERT: E 318 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7766 (mm-30) REVERT: E 330 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7003 (tp30) REVERT: E 396 GLU cc_start: 0.8747 (tt0) cc_final: 0.8144 (tp30) REVERT: E 460 GLU cc_start: 0.8461 (tp30) cc_final: 0.7994 (mm-30) REVERT: E 543 TRP cc_start: 0.8618 (t-100) cc_final: 0.8165 (m-90) REVERT: E 551 MET cc_start: 0.6031 (ptp) cc_final: 0.5191 (tmm) REVERT: E 556 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.8198 (ttm110) REVERT: E 747 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7430 (t-90) REVERT: E 821 ILE cc_start: 0.8562 (mp) cc_final: 0.8252 (mp) REVERT: F 207 GLU cc_start: 0.7218 (mp0) cc_final: 0.6838 (mp0) REVERT: F 224 ILE cc_start: 0.8133 (mm) cc_final: 0.7857 (tp) REVERT: F 299 LEU cc_start: 0.7487 (mt) cc_final: 0.6730 (pp) REVERT: F 359 LEU cc_start: 0.8516 (pp) cc_final: 0.7836 (mm) REVERT: F 392 ASP cc_start: 0.7825 (t0) cc_final: 0.7443 (t0) REVERT: F 466 LYS cc_start: 0.6996 (tttt) cc_final: 0.6639 (mptt) REVERT: F 486 ILE cc_start: -0.1324 (OUTLIER) cc_final: -0.1941 (mt) REVERT: F 498 MET cc_start: 0.6421 (tpp) cc_final: 0.5219 (mmm) REVERT: F 661 TYR cc_start: 0.6607 (m-10) cc_final: 0.6227 (m-80) REVERT: F 801 LYS cc_start: 0.8951 (pttp) cc_final: 0.8523 (mmtt) REVERT: F 850 GLU cc_start: 0.5966 (pm20) cc_final: 0.5374 (tt0) outliers start: 114 outliers final: 87 residues processed: 553 average time/residue: 0.4009 time to fit residues: 368.6070 Evaluate side-chains 544 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 451 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 288 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 331 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 831 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33321 Z= 0.224 Angle : 0.637 10.786 44970 Z= 0.315 Chirality : 0.043 0.363 5093 Planarity : 0.004 0.049 5872 Dihedral : 8.087 168.232 4741 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.23 % Allowed : 19.24 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 4053 helix: 1.17 (0.11), residues: 2330 sheet: -1.76 (0.25), residues: 447 loop : -1.48 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 462 HIS 0.008 0.001 HIS A 747 PHE 0.028 0.002 PHE C 729 TYR 0.035 0.001 TYR B 783 ARG 0.008 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 462 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8086 (tt0) REVERT: A 329 LEU cc_start: 0.9313 (tp) cc_final: 0.9001 (tt) REVERT: A 392 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8054 (t0) REVERT: A 481 GLN cc_start: 0.6744 (pt0) cc_final: 0.6292 (tt0) REVERT: A 546 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6795 (tp) REVERT: A 661 TYR cc_start: 0.8049 (t80) cc_final: 0.7747 (t80) REVERT: A 812 TYR cc_start: 0.5985 (t80) cc_final: 0.5721 (t80) REVERT: B 358 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7180 (pt0) REVERT: B 457 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8440 (tm-30) REVERT: B 524 MET cc_start: 0.1377 (mmt) cc_final: -0.0244 (ptt) REVERT: B 535 GLU cc_start: 0.7676 (mp0) cc_final: 0.7418 (mp0) REVERT: B 685 ASP cc_start: 0.7814 (p0) cc_final: 0.7315 (p0) REVERT: B 700 THR cc_start: 0.8765 (m) cc_final: 0.8289 (p) REVERT: B 747 HIS cc_start: 0.7352 (m-70) cc_final: 0.6837 (m170) REVERT: B 843 VAL cc_start: 0.8395 (t) cc_final: 0.8116 (p) REVERT: C 181 ILE cc_start: 0.9035 (mp) cc_final: 0.8778 (mt) REVERT: C 217 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 242 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: C 254 GLU cc_start: 0.8842 (tp30) cc_final: 0.8577 (tp30) REVERT: C 260 LYS cc_start: 0.9008 (tttt) cc_final: 0.8663 (tptt) REVERT: C 350 LEU cc_start: 0.9300 (mt) cc_final: 0.9092 (mt) REVERT: C 396 GLU cc_start: 0.8571 (tt0) cc_final: 0.8019 (tm-30) REVERT: C 410 GLU cc_start: 0.3843 (mp0) cc_final: 0.2743 (tt0) REVERT: C 669 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7728 (mtp85) REVERT: C 700 THR cc_start: 0.8710 (m) cc_final: 0.8355 (p) REVERT: C 716 MET cc_start: 0.7953 (mtm) cc_final: 0.7703 (mtp) REVERT: C 812 TYR cc_start: 0.7937 (m-80) cc_final: 0.7297 (m-10) REVERT: D 252 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6150 (ttt180) REVERT: D 260 LYS cc_start: 0.7424 (mmmt) cc_final: 0.6882 (tttm) REVERT: D 462 TRP cc_start: 0.4530 (t60) cc_final: 0.4323 (t60) REVERT: D 640 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8250 (ttpp) REVERT: D 647 VAL cc_start: 0.9227 (p) cc_final: 0.8939 (t) REVERT: D 677 ASP cc_start: 0.7766 (t0) cc_final: 0.7485 (t0) REVERT: D 780 LYS cc_start: 0.8872 (mttt) cc_final: 0.8549 (tmtt) REVERT: E 185 GLU cc_start: 0.8032 (tt0) cc_final: 0.7490 (tp30) REVERT: E 188 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7193 (ttp-170) REVERT: E 318 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7890 (mm-30) REVERT: E 329 LEU cc_start: 0.7669 (mt) cc_final: 0.7455 (mt) REVERT: E 330 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6999 (tp30) REVERT: E 392 ASP cc_start: 0.7935 (m-30) cc_final: 0.7715 (m-30) REVERT: E 396 GLU cc_start: 0.8732 (tt0) cc_final: 0.8140 (tp30) REVERT: E 460 GLU cc_start: 0.8483 (tp30) cc_final: 0.8063 (mm-30) REVERT: E 543 TRP cc_start: 0.8608 (t-100) cc_final: 0.8085 (m-90) REVERT: E 551 MET cc_start: 0.6015 (ptp) cc_final: 0.5671 (tmm) REVERT: E 747 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7440 (t-90) REVERT: E 821 ILE cc_start: 0.8545 (mp) cc_final: 0.8286 (mp) REVERT: F 224 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (tp) REVERT: F 241 ASP cc_start: 0.7005 (t70) cc_final: 0.6624 (p0) REVERT: F 359 LEU cc_start: 0.8595 (pp) cc_final: 0.7940 (mm) REVERT: F 486 ILE cc_start: -0.1492 (OUTLIER) cc_final: -0.2120 (mt) REVERT: F 498 MET cc_start: 0.6472 (tpp) cc_final: 0.5293 (mmm) REVERT: F 661 TYR cc_start: 0.6773 (m-10) cc_final: 0.6337 (m-80) REVERT: F 801 LYS cc_start: 0.8960 (pttp) cc_final: 0.8542 (mmtt) outliers start: 111 outliers final: 91 residues processed: 532 average time/residue: 0.4163 time to fit residues: 370.9608 Evaluate side-chains 522 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 424 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 640 LYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 270 optimal weight: 7.9990 chunk 407 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33321 Z= 0.274 Angle : 0.710 30.926 44970 Z= 0.348 Chirality : 0.044 0.340 5093 Planarity : 0.004 0.061 5872 Dihedral : 8.206 174.030 4741 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.11 % Allowed : 19.79 % Favored : 77.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.71 % 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: -0.01 (0.14), residues: 4053 helix: 1.16 (0.11), residues: 2331 sheet: -1.74 (0.25), residues: 447 loop : -1.49 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 462 HIS 0.019 0.001 HIS A 281 PHE 0.037 0.002 PHE C 729 TYR 0.034 0.001 TYR B 783 ARG 0.008 0.000 ARG A 819 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 434 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.8607 (mm) cc_final: 0.8216 (mm) REVERT: A 392 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8057 (t0) REVERT: A 481 GLN cc_start: 0.6753 (pt0) cc_final: 0.6280 (tt0) REVERT: A 546 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6595 (tp) REVERT: A 661 TYR cc_start: 0.8082 (t80) cc_final: 0.7822 (t80) REVERT: A 812 TYR cc_start: 0.5937 (t80) cc_final: 0.5669 (t80) REVERT: B 242 MET cc_start: 0.8976 (mmm) cc_final: 0.8662 (mmm) REVERT: B 358 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7298 (pt0) REVERT: B 457 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8338 (tm-30) REVERT: B 524 MET cc_start: 0.1278 (mmt) cc_final: -0.0269 (ptt) REVERT: B 535 GLU cc_start: 0.7677 (mp0) cc_final: 0.7440 (mp0) REVERT: B 685 ASP cc_start: 0.7846 (p0) cc_final: 0.7338 (p0) REVERT: B 700 THR cc_start: 0.8777 (m) cc_final: 0.8288 (p) REVERT: B 747 HIS cc_start: 0.7355 (m-70) cc_final: 0.6811 (m170) REVERT: B 843 VAL cc_start: 0.8445 (t) cc_final: 0.8235 (p) REVERT: C 181 ILE cc_start: 0.9048 (mp) cc_final: 0.8785 (mt) REVERT: C 242 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: C 254 GLU cc_start: 0.8837 (tp30) cc_final: 0.8580 (tp30) REVERT: C 260 LYS cc_start: 0.9021 (tttt) cc_final: 0.8691 (tptt) REVERT: C 396 GLU cc_start: 0.8563 (tt0) cc_final: 0.7930 (tm-30) REVERT: C 410 GLU cc_start: 0.3758 (mp0) cc_final: 0.2579 (tt0) REVERT: C 700 THR cc_start: 0.8765 (m) cc_final: 0.8386 (p) REVERT: C 716 MET cc_start: 0.7979 (mtm) cc_final: 0.7724 (mtp) REVERT: C 812 TYR cc_start: 0.7990 (m-80) cc_final: 0.7360 (m-10) REVERT: D 252 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6144 (ttt180) REVERT: D 260 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7045 (tttm) REVERT: D 283 MET cc_start: 0.7787 (tpp) cc_final: 0.7417 (tpp) REVERT: D 330 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7485 (pt0) REVERT: D 640 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8207 (ttpp) REVERT: D 647 VAL cc_start: 0.9206 (p) cc_final: 0.8911 (t) REVERT: D 677 ASP cc_start: 0.7952 (t0) cc_final: 0.7589 (t0) REVERT: D 691 LEU cc_start: 0.8346 (tp) cc_final: 0.8036 (tp) REVERT: D 780 LYS cc_start: 0.8908 (mttt) cc_final: 0.8593 (tmtt) REVERT: E 185 GLU cc_start: 0.8050 (tt0) cc_final: 0.7546 (tp30) REVERT: E 188 ARG cc_start: 0.7539 (ttm110) cc_final: 0.7205 (ttp-170) REVERT: E 318 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7897 (mm-30) REVERT: E 329 LEU cc_start: 0.7792 (mt) cc_final: 0.7382 (pt) REVERT: E 330 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7107 (tp30) REVERT: E 392 ASP cc_start: 0.7947 (m-30) cc_final: 0.7719 (m-30) REVERT: E 396 GLU cc_start: 0.8744 (tt0) cc_final: 0.8120 (tp30) REVERT: E 460 GLU cc_start: 0.8486 (tp30) cc_final: 0.8003 (mm-30) REVERT: E 543 TRP cc_start: 0.8628 (t-100) cc_final: 0.8115 (m-90) REVERT: E 551 MET cc_start: 0.6014 (ptp) cc_final: 0.5734 (tmm) REVERT: E 736 HIS cc_start: 0.6761 (p-80) cc_final: 0.6380 (t-90) REVERT: E 747 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: E 821 ILE cc_start: 0.8540 (mp) cc_final: 0.8339 (mp) REVERT: F 224 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8041 (tp) REVERT: F 241 ASP cc_start: 0.7023 (t70) cc_final: 0.6739 (p0) REVERT: F 359 LEU cc_start: 0.8639 (pp) cc_final: 0.8002 (mm) REVERT: F 486 ILE cc_start: -0.1344 (OUTLIER) cc_final: -0.1949 (mt) REVERT: F 498 MET cc_start: 0.6535 (tpp) cc_final: 0.5354 (mmm) REVERT: F 661 TYR cc_start: 0.6774 (m-10) cc_final: 0.6376 (m-80) REVERT: F 801 LYS cc_start: 0.8952 (pttp) cc_final: 0.8514 (mmtt) outliers start: 107 outliers final: 88 residues processed: 506 average time/residue: 0.4069 time to fit residues: 343.2905 Evaluate side-chains 516 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 421 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 640 LYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 299 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103169 restraints weight = 69201.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103770 restraints weight = 45974.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104371 restraints weight = 31417.304| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33321 Z= 0.233 Angle : 0.675 23.960 44970 Z= 0.330 Chirality : 0.043 0.237 5093 Planarity : 0.004 0.056 5872 Dihedral : 8.167 176.702 4741 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.00 % Allowed : 20.17 % Favored : 76.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 4053 helix: 1.19 (0.11), residues: 2334 sheet: -1.73 (0.25), residues: 434 loop : -1.50 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 462 HIS 0.022 0.001 HIS A 281 PHE 0.032 0.002 PHE C 729 TYR 0.027 0.001 TYR D 656 ARG 0.008 0.000 ARG B 819 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7811.12 seconds wall clock time: 140 minutes 27.67 seconds (8427.67 seconds total)