Starting phenix.real_space_refine on Sun Apr 14 02:03:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/04_2024/6qs7_4626_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1218 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 108 5.16 5 C 18010 2.51 5 N 5230 2.21 5 O 5487 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 "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "E PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28875 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} 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: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 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: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} 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: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} 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: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} 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: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.11, per 1000 atoms: 0.52 Number of scatterers: 28875 At special positions: 0 Unit cell: (124.95, 144.9, 157.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 32 15.00 Mg 8 11.99 O 5487 8.00 N 5230 7.00 C 18010 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.06 Conformation dependent library (CDL) restraints added in 5.0 seconds 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 26 sheets defined 51.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.60 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 195 removed outlier: 3.613A pdb=" N GLN A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.818A pdb=" N VAL A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) 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 352 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.787A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 640 through 647 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 726 Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 removed outlier: 4.094A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 255 through 268 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 removed outlier: 4.046A pdb=" N ARG B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 343 through 361 removed outlier: 5.247A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 574 through 588 Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 661 through 667 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 813 through 833 Proline residue: B 816 - end of helix removed outlier: 3.580A pdb=" N ARG B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 823 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 824 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 825 " --> pdb=" O GLN B 822 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN B 827 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Proline residue: B 828 - end of helix removed outlier: 3.796A pdb=" N ILE B 833 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.895A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 343 through 361 removed outlier: 4.300A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 445 through 464 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 566 Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 654 through 656 No H-bonds generated for 'chain 'C' and resid 654 through 656' 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 removed outlier: 3.726A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 806 Processing helix chain 'C' and resid 815 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 214 through 224 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.562A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 297 through 303 Proline residue: D 301 - end of helix No H-bonds generated for 'chain 'D' and resid 297 through 303' Processing helix chain 'D' and resid 316 through 322 removed outlier: 4.002A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 445 through 464 Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 553 through 565 removed outlier: 5.868A pdb=" N GLU D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 589 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 642 through 646 Processing helix chain 'D' and resid 654 through 656 No H-bonds generated for 'chain 'D' and resid 654 through 656' Processing helix chain 'D' and resid 662 through 668 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 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' 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 168 through 174 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 247 removed outlier: 3.590A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 247' Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 296 through 303 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.847A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 332 " --> pdb=" O LEU E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 327 through 332' Processing helix chain 'E' and resid 343 through 359 removed outlier: 4.551A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 445 through 465 Processing helix chain 'E' and resid 533 through 543 Processing helix chain 'E' and resid 553 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 662 through 668 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 687 through 696 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 734 through 748 Processing helix chain 'E' and resid 751 through 754 No H-bonds generated for 'chain 'E' and resid 751 through 754' Processing helix chain 'E' and resid 768 through 787 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 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 removed outlier: 3.949A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) 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 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 296 through 305 Proline residue: F 301 - end of helix removed outlier: 3.774A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.875A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.699A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 588 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 643 through 646 No H-bonds generated for 'chain 'F' and resid 643 through 646' Processing helix chain 'F' and resid 655 through 658 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 removed outlier: 3.965A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 728 removed outlier: 4.341A pdb=" N ASP F 723 " --> pdb=" O LEU F 720 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG F 728 " --> pdb=" O ILE F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 751 through 756 removed outlier: 4.101A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) 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 833 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.468A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 311 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 206 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 603 removed outlier: 3.641A pdb=" N PHE A 601 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 698 through 700 Processing sheet with id= D, first strand: chain 'A' and resid 793 through 795 removed outlier: 5.936A pdb=" N ILE A 844 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.365A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 202 through 206 removed outlier: 5.947A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.139A 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 599 through 604 removed outlier: 6.589A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 698 through 700 removed outlier: 3.544A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 793 through 795 removed outlier: 5.880A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 165 through 167 removed outlier: 5.094A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 599 through 602 removed outlier: 6.547A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= M, first strand: chain 'C' and resid 844 through 848 removed outlier: 3.821A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 165 through 167 removed outlier: 4.893A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY D 206 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 601 through 604 removed outlier: 6.814A pdb=" N GLU D 759 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU D 604 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 761 " --> pdb=" O LEU D 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.197A pdb=" N VAL D 713 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU D 676 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 715 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= R, first strand: chain 'D' and resid 844 through 848 Processing sheet with id= S, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.618A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 333 through 337 removed outlier: 7.619A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.652A pdb=" N LEU E 602 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.525A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 846 through 848 Processing sheet with id= X, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.822A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 311 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLN F 334 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE F 205 " --> pdb=" O GLN F 334 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL F 336 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 759 through 763 removed outlier: 3.860A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 761 " --> pdb=" O LEU F 602 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 718 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 605 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 792 through 795 1196 hydrogen bonds defined for protein. 3540 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: 10.91 Time building geometry restraints manager: 12.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10032 1.34 - 1.50: 7639 1.50 - 1.65: 11433 1.65 - 1.80: 160 1.80 - 1.95: 34 Bond restraints: 29298 Sorted by residual: bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.72e-02 3.38e+03 2.56e+01 bond pdb=" C GLY A 253 " pdb=" N GLU A 254 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" C ALA D 682 " pdb=" N HIS D 683 " ideal model delta sigma weight residual 1.333 1.224 0.108 2.74e-02 1.33e+03 1.56e+01 bond pdb=" C PHE C 749 " pdb=" N ARG C 750 " ideal model delta sigma weight residual 1.333 1.246 0.086 2.74e-02 1.33e+03 9.90e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 ... (remaining 29293 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.38: 473 104.38 - 112.26: 14694 112.26 - 120.14: 12985 120.14 - 128.02: 11239 128.02 - 135.89: 207 Bond angle restraints: 39598 Sorted by residual: angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.48 9.10 1.95e+00 2.63e-01 2.18e+01 angle pdb=" C GLY F 730 " pdb=" N GLU F 731 " pdb=" CA GLU F 731 " ideal model delta sigma weight residual 122.08 128.02 -5.94 1.47e+00 4.63e-01 1.63e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 122.46 111.80 10.66 2.70e+00 1.37e-01 1.56e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 113.18 104.14 9.04 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA LEU E 646 " pdb=" CB LEU E 646 " pdb=" CG LEU E 646 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 17560 23.96 - 47.93: 423 47.93 - 71.89: 73 71.89 - 95.85: 8 95.85 - 119.82: 2 Dihedral angle restraints: 18066 sinusoidal: 7643 harmonic: 10423 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -179.81 119.82 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.25 116.25 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 18063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3091 0.057 - 0.113: 1107 0.113 - 0.170: 252 0.170 - 0.226: 24 0.226 - 0.283: 5 Chirality restraints: 4479 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 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU B 694 " pdb=" CB LEU B 694 " pdb=" CD1 LEU B 694 " pdb=" CD2 LEU B 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL D 679 " pdb=" CA VAL D 679 " pdb=" CG1 VAL D 679 " pdb=" CG2 VAL D 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4476 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 301 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.013 2.00e-02 2.50e+03 2.18e-02 8.30e+00 pdb=" CG PHE C 763 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 823 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLN C 823 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN C 823 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 824 " 0.016 2.00e-02 2.50e+03 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 360 2.61 - 3.18: 24582 3.18 - 3.76: 44605 3.76 - 4.33: 61982 4.33 - 4.90: 101448 Nonbonded interactions: 232977 Sorted by model distance: nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.041 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.046 2.170 nonbonded pdb=" OG1 THR C 612 " pdb="MG MG C1004 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR D 612 " pdb="MG MG D1004 " model vdw 2.067 2.170 nonbonded pdb=" O1B AGS D1001 " pdb="MG MG D1003 " model vdw 2.067 2.170 ... (remaining 232972 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 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 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and (resid 159 through 287 or resid 293 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 7.160 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 77.570 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.011 0.147 29298 Z= 0.681 Angle : 1.053 14.039 39598 Z= 0.564 Chirality : 0.059 0.283 4479 Planarity : 0.008 0.074 5170 Dihedral : 11.169 119.815 11342 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.20 % Allowed : 0.76 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -3.83 (0.11), residues: 3563 helix: -2.30 (0.09), residues: 1903 sheet: -2.75 (0.25), residues: 339 loop : -2.58 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 543 HIS 0.013 0.002 HIS F 747 PHE 0.043 0.004 PHE C 763 TYR 0.037 0.003 TYR D 653 ARG 0.015 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 930 time to evaluate : 3.128 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 251 TYR cc_start: 0.8656 (m-10) cc_final: 0.7589 (m-10) REVERT: A 326 ASP cc_start: 0.8334 (t70) cc_final: 0.8082 (t0) REVERT: A 564 GLN cc_start: 0.8854 (tt0) cc_final: 0.8316 (tp-100) REVERT: A 642 SER cc_start: 0.7711 (m) cc_final: 0.7281 (p) REVERT: A 671 TYR cc_start: 0.8824 (m-80) cc_final: 0.8621 (m-80) REVERT: A 738 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7286 (pttm) REVERT: A 794 HIS cc_start: 0.7673 (m170) cc_final: 0.7074 (t70) REVERT: A 818 LYS cc_start: 0.4154 (mtpt) cc_final: 0.3930 (pttt) REVERT: A 842 LYS cc_start: 0.4084 (mttt) cc_final: 0.3825 (mmtm) REVERT: B 354 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8172 (tttm) REVERT: B 533 ASP cc_start: 0.7983 (p0) cc_final: 0.7661 (p0) REVERT: B 562 MET cc_start: 0.8927 (tpt) cc_final: 0.8702 (tpt) REVERT: B 634 MET cc_start: 0.9387 (mmm) cc_final: 0.9181 (mmm) REVERT: B 677 ASP cc_start: 0.8035 (t0) cc_final: 0.7529 (t0) REVERT: B 700 THR cc_start: 0.8368 (m) cc_final: 0.7844 (p) REVERT: B 729 PHE cc_start: 0.7758 (t80) cc_final: 0.7132 (t80) REVERT: B 779 LEU cc_start: 0.9279 (mt) cc_final: 0.8964 (mp) REVERT: B 785 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7574 (ptp-170) REVERT: B 802 LEU cc_start: 0.8709 (mp) cc_final: 0.8485 (mt) REVERT: B 818 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8817 (ttpp) REVERT: B 826 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8420 (mp0) REVERT: C 236 ARG cc_start: 0.8344 (mmt180) cc_final: 0.7966 (mmp80) REVERT: C 241 ASP cc_start: 0.7731 (t0) cc_final: 0.7311 (t0) REVERT: C 246 VAL cc_start: 0.9248 (t) cc_final: 0.8985 (p) REVERT: C 257 GLU cc_start: 0.8393 (tt0) cc_final: 0.8040 (tt0) REVERT: C 334 GLN cc_start: 0.8499 (mm110) cc_final: 0.7883 (mm-40) REVERT: C 388 ASP cc_start: 0.8750 (t70) cc_final: 0.8484 (t0) REVERT: C 423 LYS cc_start: 0.8683 (tptm) cc_final: 0.8384 (ttpt) REVERT: C 532 THR cc_start: 0.8264 (p) cc_final: 0.7998 (m) REVERT: C 692 GLN cc_start: 0.8103 (mt0) cc_final: 0.7654 (mt0) REVERT: C 705 ARG cc_start: 0.7652 (ptt-90) cc_final: 0.7201 (ptp90) REVERT: C 780 LYS cc_start: 0.9083 (mttt) cc_final: 0.8709 (tptt) REVERT: C 786 LEU cc_start: 0.9154 (mt) cc_final: 0.8921 (tp) REVERT: C 801 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8564 (ttpp) REVERT: C 826 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 161 LEU cc_start: 0.8922 (mt) cc_final: 0.8556 (mt) REVERT: D 163 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8557 (mptt) REVERT: D 265 ASP cc_start: 0.8066 (m-30) cc_final: 0.7720 (t0) REVERT: D 330 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 345 ASP cc_start: 0.8374 (m-30) cc_final: 0.7793 (m-30) REVERT: D 552 MET cc_start: 0.7720 (ptm) cc_final: 0.6985 (ppp) REVERT: D 644 SER cc_start: 0.8837 (m) cc_final: 0.8537 (p) REVERT: D 696 ASP cc_start: 0.8757 (m-30) cc_final: 0.8544 (m-30) REVERT: D 780 LYS cc_start: 0.8736 (mttt) cc_final: 0.8227 (mtmm) REVERT: D 827 ASN cc_start: 0.8692 (m-40) cc_final: 0.8065 (m110) REVERT: E 162 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8321 (pttm) REVERT: E 191 ILE cc_start: 0.8699 (mt) cc_final: 0.8398 (mm) REVERT: E 205 ILE cc_start: 0.8775 (mt) cc_final: 0.8392 (pt) REVERT: E 257 GLU cc_start: 0.8923 (tt0) cc_final: 0.8510 (mm-30) REVERT: E 359 LEU cc_start: 0.8970 (mp) cc_final: 0.8689 (mp) REVERT: E 426 GLN cc_start: 0.8706 (tt0) cc_final: 0.8352 (mt0) REVERT: E 458 LEU cc_start: 0.7723 (mt) cc_final: 0.7505 (mt) REVERT: E 568 HIS cc_start: 0.7151 (m170) cc_final: 0.6928 (m-70) REVERT: E 633 ASP cc_start: 0.8844 (m-30) cc_final: 0.8528 (m-30) REVERT: E 634 MET cc_start: 0.9076 (mmm) cc_final: 0.8800 (tpp) REVERT: E 707 VAL cc_start: 0.9405 (t) cc_final: 0.9142 (m) REVERT: E 726 GLN cc_start: 0.7752 (mt0) cc_final: 0.7280 (pt0) REVERT: F 178 ASP cc_start: 0.8100 (m-30) cc_final: 0.7653 (p0) REVERT: F 217 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6681 (mt-10) REVERT: F 330 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7324 (pt0) REVERT: F 376 LEU cc_start: 0.7946 (mt) cc_final: 0.7690 (pp) REVERT: F 393 LEU cc_start: 0.7670 (mt) cc_final: 0.7199 (mp) REVERT: F 538 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7389 (tp30) REVERT: F 563 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6313 (pt0) REVERT: F 582 ASN cc_start: 0.8946 (m-40) cc_final: 0.8659 (m-40) REVERT: F 595 ASN cc_start: 0.8543 (m-40) cc_final: 0.7792 (t0) REVERT: F 626 ASP cc_start: 0.7472 (m-30) cc_final: 0.6971 (p0) REVERT: F 629 MET cc_start: 0.8167 (ptm) cc_final: 0.7787 (ptp) REVERT: F 630 VAL cc_start: 0.8421 (t) cc_final: 0.7929 (t) REVERT: F 631 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7529 (ttt180) REVERT: F 638 MET cc_start: 0.7561 (mtm) cc_final: 0.7342 (mmm) REVERT: F 691 LEU cc_start: 0.9074 (mt) cc_final: 0.8840 (pp) REVERT: F 736 HIS cc_start: 0.8428 (m170) cc_final: 0.8040 (m-70) REVERT: F 821 ILE cc_start: 0.8900 (mt) cc_final: 0.8327 (mt) outliers start: 6 outliers final: 1 residues processed: 936 average time/residue: 0.5355 time to fit residues: 731.2213 Evaluate side-chains 481 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 480 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 748 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 201 ASN D 567 HIS D 620 ASN D 641 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 GLN D 748 ASN D 822 GLN E 297 ASN E 309 HIS E 334 GLN E 620 ASN E 641 HIS ** E 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS F 309 HIS ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 776 GLN F 849 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29298 Z= 0.202 Angle : 0.668 13.469 39598 Z= 0.332 Chirality : 0.044 0.232 4479 Planarity : 0.005 0.052 5170 Dihedral : 9.913 98.006 4209 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.36 % Allowed : 9.21 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -2.27 (0.13), residues: 3563 helix: -0.84 (0.11), residues: 1907 sheet: -2.45 (0.25), residues: 370 loop : -2.04 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 543 HIS 0.009 0.001 HIS B 747 PHE 0.018 0.001 PHE F 729 TYR 0.026 0.002 TYR B 783 ARG 0.009 0.001 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 562 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7399 (ttpt) REVERT: A 251 TYR cc_start: 0.8509 (m-10) cc_final: 0.7446 (m-10) REVERT: A 265 ASP cc_start: 0.8468 (m-30) cc_final: 0.8243 (m-30) REVERT: A 564 GLN cc_start: 0.8898 (tt0) cc_final: 0.8329 (tp-100) REVERT: A 642 SER cc_start: 0.7523 (m) cc_final: 0.7049 (p) REVERT: A 794 HIS cc_start: 0.7705 (m170) cc_final: 0.7120 (t70) REVERT: A 842 LYS cc_start: 0.4249 (mttt) cc_final: 0.3917 (mmtm) REVERT: B 236 ARG cc_start: 0.7392 (tpp80) cc_final: 0.7048 (tpt170) REVERT: B 241 ASP cc_start: 0.8217 (t0) cc_final: 0.7741 (t0) REVERT: B 298 MET cc_start: 0.8838 (mtp) cc_final: 0.8566 (mtp) REVERT: B 533 ASP cc_start: 0.7977 (p0) cc_final: 0.7707 (p0) REVERT: B 700 THR cc_start: 0.8477 (m) cc_final: 0.7902 (p) REVERT: B 785 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7645 (ptp-170) REVERT: B 831 GLN cc_start: 0.8624 (tp40) cc_final: 0.8103 (tm-30) REVERT: C 236 ARG cc_start: 0.8416 (mmt180) cc_final: 0.8093 (mmp80) REVERT: C 241 ASP cc_start: 0.7588 (t0) cc_final: 0.7131 (t0) REVERT: C 257 GLU cc_start: 0.8287 (tt0) cc_final: 0.8023 (tt0) REVERT: C 334 GLN cc_start: 0.8259 (mm110) cc_final: 0.7504 (mm-40) REVERT: C 388 ASP cc_start: 0.8686 (t70) cc_final: 0.8378 (t0) REVERT: C 421 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: C 780 LYS cc_start: 0.9124 (mttt) cc_final: 0.8768 (tptt) REVERT: C 801 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8603 (ttpp) REVERT: D 161 LEU cc_start: 0.8751 (mt) cc_final: 0.8357 (mt) REVERT: D 163 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8587 (mptt) REVERT: D 265 ASP cc_start: 0.7915 (m-30) cc_final: 0.7636 (t0) REVERT: D 315 THR cc_start: 0.9205 (m) cc_final: 0.8995 (p) REVERT: D 330 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7864 (tm-30) REVERT: D 345 ASP cc_start: 0.8426 (m-30) cc_final: 0.7890 (m-30) REVERT: D 392 ASP cc_start: 0.8220 (m-30) cc_final: 0.7979 (m-30) REVERT: D 552 MET cc_start: 0.7353 (ptm) cc_final: 0.6883 (ppp) REVERT: D 644 SER cc_start: 0.9003 (m) cc_final: 0.8779 (p) REVERT: D 827 ASN cc_start: 0.8669 (m-40) cc_final: 0.7996 (m110) REVERT: E 162 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8361 (pttm) REVERT: E 185 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: E 257 GLU cc_start: 0.8865 (tt0) cc_final: 0.8575 (mm-30) REVERT: E 329 LEU cc_start: 0.7576 (tp) cc_final: 0.7125 (tp) REVERT: E 359 LEU cc_start: 0.8911 (mp) cc_final: 0.8508 (mp) REVERT: E 426 GLN cc_start: 0.8584 (tt0) cc_final: 0.8282 (mt0) REVERT: E 565 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7353 (tp30) REVERT: E 707 VAL cc_start: 0.9375 (t) cc_final: 0.9009 (m) REVERT: E 726 GLN cc_start: 0.7555 (mt0) cc_final: 0.7240 (pt0) REVERT: F 178 ASP cc_start: 0.8201 (m-30) cc_final: 0.7764 (p0) REVERT: F 217 GLU cc_start: 0.7982 (mt-10) cc_final: 0.6787 (mt-10) REVERT: F 257 GLU cc_start: 0.8451 (tt0) cc_final: 0.8250 (tm-30) REVERT: F 318 GLU cc_start: 0.7902 (mp0) cc_final: 0.7499 (mp0) REVERT: F 322 TYR cc_start: 0.7683 (m-80) cc_final: 0.7258 (m-80) REVERT: F 330 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7132 (pt0) REVERT: F 364 GLN cc_start: 0.8214 (mt0) cc_final: 0.7944 (tm-30) REVERT: F 376 LEU cc_start: 0.8081 (mt) cc_final: 0.7876 (tt) REVERT: F 538 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7565 (tp30) REVERT: F 540 LEU cc_start: 0.8257 (mm) cc_final: 0.7777 (mm) REVERT: F 582 ASN cc_start: 0.8967 (m-40) cc_final: 0.8716 (m-40) REVERT: F 595 ASN cc_start: 0.8539 (m-40) cc_final: 0.7790 (t0) REVERT: F 626 ASP cc_start: 0.7197 (m-30) cc_final: 0.6979 (p0) REVERT: F 629 MET cc_start: 0.8189 (ptm) cc_final: 0.7858 (ptp) REVERT: F 634 MET cc_start: 0.7157 (mpp) cc_final: 0.6945 (mmp) REVERT: F 638 MET cc_start: 0.7520 (mtm) cc_final: 0.7095 (mmt) REVERT: F 715 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7821 (mp) REVERT: F 746 SER cc_start: 0.8992 (m) cc_final: 0.8779 (p) REVERT: F 821 ILE cc_start: 0.8978 (mt) cc_final: 0.8690 (mt) outliers start: 71 outliers final: 35 residues processed: 607 average time/residue: 0.4424 time to fit residues: 417.6308 Evaluate side-chains 481 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 443 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 291 optimal weight: 0.0980 chunk 324 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN C 726 GLN C 794 HIS ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 831 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN E 309 HIS E 822 GLN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29298 Z= 0.296 Angle : 0.658 14.319 39598 Z= 0.327 Chirality : 0.044 0.242 4479 Planarity : 0.005 0.051 5170 Dihedral : 9.567 84.861 4209 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.83 % Allowed : 12.10 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3563 helix: -0.25 (0.11), residues: 1949 sheet: -2.48 (0.25), residues: 359 loop : -1.79 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 543 HIS 0.007 0.001 HIS C 794 PHE 0.016 0.002 PHE E 621 TYR 0.020 0.002 TYR D 653 ARG 0.007 0.000 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 446 time to evaluate : 2.914 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 250 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7393 (ttpt) REVERT: A 251 TYR cc_start: 0.8469 (m-10) cc_final: 0.7489 (m-10) REVERT: A 564 GLN cc_start: 0.8905 (tt0) cc_final: 0.8340 (tp-100) REVERT: A 641 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6345 (p-80) REVERT: A 794 HIS cc_start: 0.7668 (m170) cc_final: 0.7086 (t70) REVERT: A 842 LYS cc_start: 0.4243 (mttt) cc_final: 0.3868 (mmtm) REVERT: B 167 ASP cc_start: 0.8032 (t0) cc_final: 0.7714 (t0) REVERT: B 236 ARG cc_start: 0.7404 (tpp80) cc_final: 0.7125 (tpt170) REVERT: B 254 GLU cc_start: 0.7925 (tt0) cc_final: 0.7670 (tt0) REVERT: B 298 MET cc_start: 0.8895 (mtp) cc_final: 0.8639 (mtp) REVERT: B 533 ASP cc_start: 0.8044 (p0) cc_final: 0.7718 (p0) REVERT: B 562 MET cc_start: 0.8862 (mmm) cc_final: 0.8559 (mmm) REVERT: B 700 THR cc_start: 0.8561 (m) cc_final: 0.8284 (m) REVERT: B 808 TYR cc_start: 0.5949 (t80) cc_final: 0.5072 (t80) REVERT: C 241 ASP cc_start: 0.7742 (t0) cc_final: 0.7295 (t0) REVERT: C 257 GLU cc_start: 0.8354 (tt0) cc_final: 0.8100 (tt0) REVERT: C 388 ASP cc_start: 0.8762 (t70) cc_final: 0.8521 (t0) REVERT: C 633 ASP cc_start: 0.8001 (p0) cc_final: 0.7715 (p0) REVERT: C 780 LYS cc_start: 0.9114 (mttt) cc_final: 0.8762 (tptt) REVERT: D 161 LEU cc_start: 0.8765 (mt) cc_final: 0.8193 (mt) REVERT: D 163 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8480 (mptt) REVERT: D 265 ASP cc_start: 0.7888 (m-30) cc_final: 0.7570 (t0) REVERT: D 315 THR cc_start: 0.9248 (m) cc_final: 0.9005 (p) REVERT: D 392 ASP cc_start: 0.8252 (m-30) cc_final: 0.7990 (m-30) REVERT: D 410 GLU cc_start: 0.7879 (pm20) cc_final: 0.7566 (tt0) REVERT: D 552 MET cc_start: 0.7198 (ptm) cc_final: 0.6681 (tmm) REVERT: D 827 ASN cc_start: 0.8678 (m-40) cc_final: 0.8075 (m110) REVERT: E 162 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8384 (pttm) REVERT: E 242 MET cc_start: 0.7929 (mmt) cc_final: 0.7642 (mmt) REVERT: E 257 GLU cc_start: 0.8867 (tt0) cc_final: 0.8584 (mm-30) REVERT: E 268 LYS cc_start: 0.7199 (tttt) cc_final: 0.6604 (pttm) REVERT: E 359 LEU cc_start: 0.9021 (mp) cc_final: 0.8695 (mp) REVERT: E 426 GLN cc_start: 0.8570 (tt0) cc_final: 0.7895 (mt0) REVERT: E 707 VAL cc_start: 0.9435 (t) cc_final: 0.9048 (m) REVERT: E 726 GLN cc_start: 0.7588 (mt0) cc_final: 0.7244 (pt0) REVERT: E 822 GLN cc_start: 0.8491 (tt0) cc_final: 0.8063 (tp40) REVERT: F 178 ASP cc_start: 0.8149 (m-30) cc_final: 0.7911 (p0) REVERT: F 217 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7166 (mt-10) REVERT: F 257 GLU cc_start: 0.8457 (tt0) cc_final: 0.8202 (tm-30) REVERT: F 318 GLU cc_start: 0.7946 (mp0) cc_final: 0.7648 (mp0) REVERT: F 322 TYR cc_start: 0.7656 (m-80) cc_final: 0.7394 (m-80) REVERT: F 330 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7063 (pt0) REVERT: F 364 GLN cc_start: 0.8220 (mt0) cc_final: 0.7890 (tm-30) REVERT: F 538 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8092 (tm-30) REVERT: F 563 GLU cc_start: 0.7768 (tp30) cc_final: 0.7546 (tp30) REVERT: F 582 ASN cc_start: 0.8989 (m-40) cc_final: 0.8710 (m-40) REVERT: F 588 ARG cc_start: 0.8564 (mmt90) cc_final: 0.8064 (ptt90) REVERT: F 595 ASN cc_start: 0.8595 (m-40) cc_final: 0.7867 (t0) REVERT: F 626 ASP cc_start: 0.7287 (m-30) cc_final: 0.7067 (p0) REVERT: F 629 MET cc_start: 0.8304 (ptm) cc_final: 0.7990 (ptm) REVERT: F 715 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7825 (mp) REVERT: F 742 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7910 (mm) REVERT: F 746 SER cc_start: 0.8969 (m) cc_final: 0.8717 (p) REVERT: F 821 ILE cc_start: 0.8994 (mt) cc_final: 0.8706 (mt) outliers start: 85 outliers final: 52 residues processed: 499 average time/residue: 0.4209 time to fit residues: 331.6163 Evaluate side-chains 453 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 398 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 156 optimal weight: 0.0270 chunk 219 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN C 421 GLN C 692 GLN C 794 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29298 Z= 0.174 Angle : 0.583 15.098 39598 Z= 0.287 Chirality : 0.042 0.224 4479 Planarity : 0.004 0.051 5170 Dihedral : 9.121 72.452 4209 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.83 % Allowed : 12.83 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3563 helix: 0.30 (0.12), residues: 1918 sheet: -2.30 (0.25), residues: 371 loop : -1.61 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 543 HIS 0.010 0.001 HIS E 568 PHE 0.028 0.001 PHE C 729 TYR 0.021 0.001 TYR B 783 ARG 0.004 0.000 ARG E 728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 474 time to evaluate : 3.434 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 251 TYR cc_start: 0.8416 (m-10) cc_final: 0.7719 (m-10) REVERT: A 533 ASP cc_start: 0.6956 (p0) cc_final: 0.6748 (p0) REVERT: A 564 GLN cc_start: 0.8918 (tt0) cc_final: 0.8307 (tp-100) REVERT: A 641 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6397 (p-80) REVERT: A 794 HIS cc_start: 0.7662 (m170) cc_final: 0.7075 (t70) REVERT: A 842 LYS cc_start: 0.4290 (mttt) cc_final: 0.3880 (mmtm) REVERT: B 254 GLU cc_start: 0.7926 (tt0) cc_final: 0.7576 (tt0) REVERT: B 298 MET cc_start: 0.8815 (mtp) cc_final: 0.8572 (mtp) REVERT: B 533 ASP cc_start: 0.8047 (p0) cc_final: 0.7751 (p0) REVERT: B 562 MET cc_start: 0.8866 (mmm) cc_final: 0.8663 (mmm) REVERT: B 700 THR cc_start: 0.8572 (m) cc_final: 0.8279 (m) REVERT: B 808 TYR cc_start: 0.5817 (t80) cc_final: 0.5047 (t80) REVERT: B 831 GLN cc_start: 0.8744 (tp40) cc_final: 0.8192 (tm-30) REVERT: C 241 ASP cc_start: 0.7745 (t0) cc_final: 0.7284 (t0) REVERT: C 257 GLU cc_start: 0.8362 (tt0) cc_final: 0.8107 (tt0) REVERT: C 388 ASP cc_start: 0.8765 (t70) cc_final: 0.8544 (t0) REVERT: C 633 ASP cc_start: 0.8033 (p0) cc_final: 0.7718 (p0) REVERT: C 737 MET cc_start: 0.8598 (tpp) cc_final: 0.8174 (tpp) REVERT: C 780 LYS cc_start: 0.9117 (mttt) cc_final: 0.8763 (tptt) REVERT: D 161 LEU cc_start: 0.8668 (mt) cc_final: 0.8080 (mt) REVERT: D 163 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8472 (mptt) REVERT: D 265 ASP cc_start: 0.7723 (m-30) cc_final: 0.7494 (t0) REVERT: D 315 THR cc_start: 0.9271 (m) cc_final: 0.9016 (p) REVERT: D 392 ASP cc_start: 0.8202 (m-30) cc_final: 0.7998 (m-30) REVERT: D 410 GLU cc_start: 0.7662 (pm20) cc_final: 0.7397 (tt0) REVERT: D 551 MET cc_start: 0.7230 (mmm) cc_final: 0.5316 (mmp) REVERT: D 552 MET cc_start: 0.7055 (ptm) cc_final: 0.6569 (tmm) REVERT: D 710 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8450 (mtp85) REVERT: D 827 ASN cc_start: 0.8660 (m-40) cc_final: 0.8095 (m110) REVERT: E 162 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8353 (pttm) REVERT: E 257 GLU cc_start: 0.8810 (tt0) cc_final: 0.8573 (mm-30) REVERT: E 268 LYS cc_start: 0.7225 (tttt) cc_final: 0.6726 (pttm) REVERT: E 318 GLU cc_start: 0.8828 (mp0) cc_final: 0.8427 (mp0) REVERT: E 359 LEU cc_start: 0.8985 (mp) cc_final: 0.8654 (mp) REVERT: E 562 MET cc_start: 0.6149 (tmm) cc_final: 0.5800 (tmm) REVERT: E 596 ARG cc_start: 0.8629 (mtp180) cc_final: 0.8321 (mtp-110) REVERT: E 707 VAL cc_start: 0.9396 (t) cc_final: 0.9022 (m) REVERT: E 726 GLN cc_start: 0.7522 (mt0) cc_final: 0.7232 (pt0) REVERT: E 822 GLN cc_start: 0.8312 (tt0) cc_final: 0.8080 (tp40) REVERT: F 178 ASP cc_start: 0.8153 (m-30) cc_final: 0.7917 (p0) REVERT: F 217 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7219 (mt-10) REVERT: F 257 GLU cc_start: 0.8441 (tt0) cc_final: 0.8186 (tm-30) REVERT: F 318 GLU cc_start: 0.7863 (mp0) cc_final: 0.7650 (mp0) REVERT: F 322 TYR cc_start: 0.7654 (m-80) cc_final: 0.7405 (m-80) REVERT: F 330 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7219 (pt0) REVERT: F 538 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8020 (tm-30) REVERT: F 582 ASN cc_start: 0.8971 (m-40) cc_final: 0.8723 (m-40) REVERT: F 595 ASN cc_start: 0.8656 (m-40) cc_final: 0.7894 (t0) REVERT: F 622 MET cc_start: 0.8253 (mtm) cc_final: 0.7923 (mtm) REVERT: F 629 MET cc_start: 0.8249 (ptm) cc_final: 0.7935 (ptm) REVERT: F 715 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7877 (mp) REVERT: F 737 MET cc_start: 0.8818 (mmp) cc_final: 0.8611 (mmm) REVERT: F 742 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (mm) REVERT: F 819 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8263 (tpt-90) REVERT: F 821 ILE cc_start: 0.8987 (mt) cc_final: 0.8699 (mt) outliers start: 85 outliers final: 48 residues processed: 520 average time/residue: 0.4320 time to fit residues: 355.4750 Evaluate side-chains 464 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 412 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 421 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN E 309 HIS E 857 GLN F 595 ASN F 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 29298 Z= 0.383 Angle : 0.680 14.156 39598 Z= 0.336 Chirality : 0.046 0.180 4479 Planarity : 0.005 0.051 5170 Dihedral : 9.096 73.787 4209 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.19 % Allowed : 13.53 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.92 (0.14), residues: 3563 helix: 0.37 (0.12), residues: 1948 sheet: -2.30 (0.25), residues: 399 loop : -1.49 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 543 HIS 0.008 0.001 HIS E 568 PHE 0.019 0.002 PHE D 729 TYR 0.020 0.002 TYR D 653 ARG 0.006 0.001 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 410 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7515 (ttpt) REVERT: A 251 TYR cc_start: 0.8510 (m-10) cc_final: 0.7439 (m-10) REVERT: A 533 ASP cc_start: 0.6963 (p0) cc_final: 0.6738 (p0) REVERT: A 564 GLN cc_start: 0.8960 (tt0) cc_final: 0.8345 (tp-100) REVERT: A 641 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6540 (p-80) REVERT: A 794 HIS cc_start: 0.7667 (m170) cc_final: 0.7066 (t70) REVERT: A 842 LYS cc_start: 0.4444 (mttt) cc_final: 0.4050 (mmtm) REVERT: B 217 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8056 (mp0) REVERT: B 254 GLU cc_start: 0.8051 (tt0) cc_final: 0.7637 (tt0) REVERT: B 298 MET cc_start: 0.8912 (mtp) cc_final: 0.8654 (mtp) REVERT: B 533 ASP cc_start: 0.8113 (p0) cc_final: 0.7765 (p0) REVERT: B 562 MET cc_start: 0.8898 (mmm) cc_final: 0.8655 (mmm) REVERT: B 581 SER cc_start: 0.9334 (m) cc_final: 0.8796 (p) REVERT: B 642 SER cc_start: 0.9191 (m) cc_final: 0.8280 (p) REVERT: B 700 THR cc_start: 0.8609 (m) cc_final: 0.8338 (m) REVERT: B 808 TYR cc_start: 0.5789 (t80) cc_final: 0.5182 (t80) REVERT: C 241 ASP cc_start: 0.7866 (t0) cc_final: 0.7475 (t0) REVERT: C 257 GLU cc_start: 0.8299 (tt0) cc_final: 0.8014 (tt0) REVERT: C 664 GLU cc_start: 0.7112 (pt0) cc_final: 0.6911 (pt0) REVERT: C 780 LYS cc_start: 0.9122 (mttt) cc_final: 0.8798 (tptt) REVERT: C 786 LEU cc_start: 0.9526 (tp) cc_final: 0.9243 (tp) REVERT: D 161 LEU cc_start: 0.8655 (mt) cc_final: 0.8004 (mt) REVERT: D 163 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8483 (mptt) REVERT: D 265 ASP cc_start: 0.7870 (m-30) cc_final: 0.7589 (t0) REVERT: D 552 MET cc_start: 0.7141 (ptm) cc_final: 0.6745 (tmm) REVERT: D 710 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8421 (mtp85) REVERT: D 827 ASN cc_start: 0.8701 (m-40) cc_final: 0.8184 (m110) REVERT: E 162 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8384 (pttm) REVERT: E 257 GLU cc_start: 0.8864 (tt0) cc_final: 0.8603 (mm-30) REVERT: E 268 LYS cc_start: 0.7298 (tttt) cc_final: 0.6878 (pttm) REVERT: E 318 GLU cc_start: 0.8805 (mp0) cc_final: 0.8430 (mp0) REVERT: E 359 LEU cc_start: 0.9062 (mp) cc_final: 0.8772 (mp) REVERT: E 707 VAL cc_start: 0.9448 (t) cc_final: 0.9071 (m) REVERT: E 726 GLN cc_start: 0.7625 (mt0) cc_final: 0.7253 (pt0) REVERT: E 800 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8544 (mp) REVERT: F 178 ASP cc_start: 0.8247 (m-30) cc_final: 0.7995 (p0) REVERT: F 217 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7520 (mt-10) REVERT: F 330 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7239 (pt0) REVERT: F 376 LEU cc_start: 0.8328 (mm) cc_final: 0.8102 (pp) REVERT: F 538 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8033 (tm-30) REVERT: F 582 ASN cc_start: 0.9044 (m-40) cc_final: 0.8751 (m-40) REVERT: F 595 ASN cc_start: 0.8725 (m110) cc_final: 0.7931 (t0) REVERT: F 629 MET cc_start: 0.8402 (ptm) cc_final: 0.8133 (ptm) REVERT: F 715 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7790 (mp) REVERT: F 819 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8169 (tpt-90) REVERT: F 821 ILE cc_start: 0.8963 (mt) cc_final: 0.8677 (mt) REVERT: F 851 ASP cc_start: 0.8615 (t70) cc_final: 0.8298 (t0) outliers start: 96 outliers final: 66 residues processed: 474 average time/residue: 0.4165 time to fit residues: 318.6925 Evaluate side-chains 446 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 376 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 348 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 0.0970 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 641 HIS C 688 ASN C 692 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29298 Z= 0.178 Angle : 0.586 15.743 39598 Z= 0.287 Chirality : 0.042 0.159 4479 Planarity : 0.004 0.054 5170 Dihedral : 8.751 70.056 4209 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.93 % Allowed : 14.43 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3563 helix: 0.63 (0.12), residues: 1949 sheet: -2.16 (0.26), residues: 372 loop : -1.34 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 543 HIS 0.008 0.001 HIS E 568 PHE 0.027 0.001 PHE C 729 TYR 0.016 0.001 TYR F 164 ARG 0.004 0.000 ARG E 698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 425 time to evaluate : 3.542 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 250 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7348 (ttpt) REVERT: A 251 TYR cc_start: 0.8474 (m-10) cc_final: 0.7383 (m-10) REVERT: A 533 ASP cc_start: 0.6944 (p0) cc_final: 0.6731 (p0) REVERT: A 564 GLN cc_start: 0.8945 (tt0) cc_final: 0.8309 (tp-100) REVERT: A 641 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6467 (p-80) REVERT: A 664 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8695 (pt0) REVERT: A 794 HIS cc_start: 0.7693 (m170) cc_final: 0.7091 (t70) REVERT: A 842 LYS cc_start: 0.4415 (mttt) cc_final: 0.4036 (mmtm) REVERT: B 254 GLU cc_start: 0.7985 (tt0) cc_final: 0.7535 (tt0) REVERT: B 293 MET cc_start: 0.7640 (mtp) cc_final: 0.7408 (mtm) REVERT: B 298 MET cc_start: 0.8865 (mtp) cc_final: 0.8599 (mtp) REVERT: B 533 ASP cc_start: 0.8094 (p0) cc_final: 0.7761 (p0) REVERT: B 581 SER cc_start: 0.9285 (m) cc_final: 0.8767 (p) REVERT: B 642 SER cc_start: 0.9192 (m) cc_final: 0.8220 (p) REVERT: B 700 THR cc_start: 0.8599 (m) cc_final: 0.8362 (m) REVERT: B 808 TYR cc_start: 0.5722 (t80) cc_final: 0.5059 (t80) REVERT: C 241 ASP cc_start: 0.7726 (t0) cc_final: 0.7345 (t0) REVERT: C 257 GLU cc_start: 0.8303 (tt0) cc_final: 0.7995 (tt0) REVERT: C 421 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: C 633 ASP cc_start: 0.7866 (p0) cc_final: 0.7478 (p0) REVERT: C 780 LYS cc_start: 0.9120 (mttt) cc_final: 0.8774 (tptt) REVERT: C 786 LEU cc_start: 0.9518 (tp) cc_final: 0.9224 (tp) REVERT: D 161 LEU cc_start: 0.8602 (mt) cc_final: 0.7900 (mt) REVERT: D 163 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8508 (mptt) REVERT: D 265 ASP cc_start: 0.7741 (m-30) cc_final: 0.7508 (t0) REVERT: D 315 THR cc_start: 0.9269 (m) cc_final: 0.8968 (p) REVERT: D 392 ASP cc_start: 0.8135 (m-30) cc_final: 0.7878 (m-30) REVERT: D 551 MET cc_start: 0.6873 (mmm) cc_final: 0.6199 (mmm) REVERT: D 552 MET cc_start: 0.6862 (ptm) cc_final: 0.6282 (tmm) REVERT: D 710 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8468 (mtp85) REVERT: D 827 ASN cc_start: 0.8652 (m-40) cc_final: 0.8112 (m110) REVERT: E 162 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8381 (pttm) REVERT: E 242 MET cc_start: 0.7679 (mmt) cc_final: 0.7301 (mmt) REVERT: E 246 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8222 (m) REVERT: E 257 GLU cc_start: 0.8864 (tt0) cc_final: 0.8598 (mm-30) REVERT: E 268 LYS cc_start: 0.7267 (tttt) cc_final: 0.6846 (pttm) REVERT: E 298 MET cc_start: 0.7505 (mtp) cc_final: 0.7115 (mtt) REVERT: E 317 ASP cc_start: 0.8606 (m-30) cc_final: 0.8356 (m-30) REVERT: E 318 GLU cc_start: 0.8867 (mp0) cc_final: 0.8505 (mp0) REVERT: E 359 LEU cc_start: 0.9022 (mp) cc_final: 0.8731 (mp) REVERT: E 567 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7777 (t-90) REVERT: E 707 VAL cc_start: 0.9391 (t) cc_final: 0.9010 (m) REVERT: E 726 GLN cc_start: 0.7602 (mt0) cc_final: 0.7272 (pt0) REVERT: F 178 ASP cc_start: 0.8263 (m-30) cc_final: 0.7995 (p0) REVERT: F 217 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 254 GLU cc_start: 0.5888 (tp30) cc_final: 0.5450 (tp30) REVERT: F 330 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7226 (pt0) REVERT: F 376 LEU cc_start: 0.8316 (mm) cc_final: 0.8094 (pp) REVERT: F 538 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8047 (tm-30) REVERT: F 582 ASN cc_start: 0.9001 (m-40) cc_final: 0.8697 (m-40) REVERT: F 595 ASN cc_start: 0.8706 (m110) cc_final: 0.7982 (t0) REVERT: F 622 MET cc_start: 0.8287 (mtm) cc_final: 0.7954 (mtm) REVERT: F 629 MET cc_start: 0.8335 (ptm) cc_final: 0.7982 (ptm) REVERT: F 661 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5839 (t80) REVERT: F 821 ILE cc_start: 0.8982 (mt) cc_final: 0.8699 (mt) outliers start: 88 outliers final: 63 residues processed: 482 average time/residue: 0.4183 time to fit residues: 323.3819 Evaluate side-chains 448 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 379 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 198 optimal weight: 0.5980 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 293 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29298 Z= 0.177 Angle : 0.587 17.063 39598 Z= 0.286 Chirality : 0.042 0.181 4479 Planarity : 0.004 0.054 5170 Dihedral : 8.480 67.351 4209 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.03 % Allowed : 15.36 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3563 helix: 0.77 (0.12), residues: 1949 sheet: -2.08 (0.26), residues: 372 loop : -1.25 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 543 HIS 0.007 0.001 HIS E 568 PHE 0.038 0.001 PHE C 729 TYR 0.031 0.001 TYR B 783 ARG 0.005 0.000 ARG F 819 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 406 time to evaluate : 3.810 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 217 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8296 (tp30) REVERT: A 250 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7270 (ttpt) REVERT: A 251 TYR cc_start: 0.8454 (m-10) cc_final: 0.7337 (m-10) REVERT: A 564 GLN cc_start: 0.8925 (tt0) cc_final: 0.8303 (tp-100) REVERT: A 641 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6371 (p-80) REVERT: A 664 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8698 (pt0) REVERT: A 794 HIS cc_start: 0.7669 (m170) cc_final: 0.7085 (t70) REVERT: A 842 LYS cc_start: 0.4403 (mttt) cc_final: 0.3998 (mmtm) REVERT: B 200 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 254 GLU cc_start: 0.7984 (tt0) cc_final: 0.7531 (tt0) REVERT: B 298 MET cc_start: 0.8856 (mtp) cc_final: 0.8570 (mtp) REVERT: B 392 ASP cc_start: 0.8615 (m-30) cc_final: 0.8019 (t0) REVERT: B 533 ASP cc_start: 0.8074 (p0) cc_final: 0.7738 (p0) REVERT: B 581 SER cc_start: 0.9275 (m) cc_final: 0.8986 (p) REVERT: B 633 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7149 (p0) REVERT: B 636 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: B 642 SER cc_start: 0.9246 (m) cc_final: 0.8255 (p) REVERT: B 700 THR cc_start: 0.8588 (m) cc_final: 0.8324 (m) REVERT: B 808 TYR cc_start: 0.5817 (t80) cc_final: 0.5256 (t80) REVERT: C 241 ASP cc_start: 0.7694 (t0) cc_final: 0.7341 (t0) REVERT: C 257 GLU cc_start: 0.8292 (tt0) cc_final: 0.7998 (tt0) REVERT: C 538 GLU cc_start: 0.8137 (tp30) cc_final: 0.7895 (tm-30) REVERT: C 729 PHE cc_start: 0.8158 (t80) cc_final: 0.7954 (t80) REVERT: C 780 LYS cc_start: 0.9120 (mttt) cc_final: 0.8775 (tptt) REVERT: C 786 LEU cc_start: 0.9528 (tp) cc_final: 0.9218 (tp) REVERT: C 827 ASN cc_start: 0.8713 (m-40) cc_final: 0.8253 (m110) REVERT: D 161 LEU cc_start: 0.8565 (mt) cc_final: 0.7843 (mt) REVERT: D 163 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8500 (mptt) REVERT: D 392 ASP cc_start: 0.8118 (m-30) cc_final: 0.7880 (m-30) REVERT: D 551 MET cc_start: 0.6847 (mmm) cc_final: 0.6252 (mmm) REVERT: D 552 MET cc_start: 0.6778 (ptm) cc_final: 0.6089 (tmm) REVERT: D 710 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8437 (mtp85) REVERT: D 794 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7874 (m-70) REVERT: D 827 ASN cc_start: 0.8628 (m-40) cc_final: 0.8073 (m110) REVERT: E 162 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8340 (pttm) REVERT: E 242 MET cc_start: 0.7629 (mmt) cc_final: 0.7261 (mmt) REVERT: E 257 GLU cc_start: 0.8868 (tt0) cc_final: 0.8600 (mm-30) REVERT: E 268 LYS cc_start: 0.7278 (tttt) cc_final: 0.6863 (pttm) REVERT: E 298 MET cc_start: 0.7544 (mtp) cc_final: 0.7256 (mtt) REVERT: E 317 ASP cc_start: 0.8628 (m-30) cc_final: 0.8362 (m-30) REVERT: E 318 GLU cc_start: 0.8839 (mp0) cc_final: 0.8456 (mp0) REVERT: E 359 LEU cc_start: 0.9020 (mp) cc_final: 0.8658 (mp) REVERT: E 567 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7717 (t-90) REVERT: E 707 VAL cc_start: 0.9374 (t) cc_final: 0.8999 (m) REVERT: E 726 GLN cc_start: 0.7594 (mt0) cc_final: 0.7236 (pt0) REVERT: E 745 VAL cc_start: 0.8629 (t) cc_final: 0.8395 (p) REVERT: F 178 ASP cc_start: 0.8283 (m-30) cc_final: 0.7920 (p0) REVERT: F 217 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7551 (mt-10) REVERT: F 254 GLU cc_start: 0.5871 (tp30) cc_final: 0.5496 (tp30) REVERT: F 330 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7253 (pt0) REVERT: F 376 LEU cc_start: 0.8293 (mm) cc_final: 0.8077 (pp) REVERT: F 538 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8062 (tm-30) REVERT: F 582 ASN cc_start: 0.8997 (m-40) cc_final: 0.8687 (m-40) REVERT: F 629 MET cc_start: 0.8330 (ptm) cc_final: 0.7981 (ptm) REVERT: F 658 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6010 (pm20) REVERT: F 661 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5541 (t80) REVERT: F 821 ILE cc_start: 0.8985 (mt) cc_final: 0.8701 (mt) outliers start: 91 outliers final: 64 residues processed: 466 average time/residue: 0.4280 time to fit residues: 320.0417 Evaluate side-chains 450 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 377 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN C 748 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29298 Z= 0.208 Angle : 0.592 17.456 39598 Z= 0.289 Chirality : 0.043 0.239 4479 Planarity : 0.004 0.055 5170 Dihedral : 8.309 65.837 4209 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.79 % Allowed : 15.92 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3563 helix: 0.90 (0.12), residues: 1948 sheet: -2.02 (0.25), residues: 382 loop : -1.16 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 543 HIS 0.006 0.001 HIS B 770 PHE 0.031 0.002 PHE D 276 TYR 0.031 0.001 TYR A 656 ARG 0.005 0.000 ARG E 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 391 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8181 (tp30) cc_final: 0.7853 (tp30) REVERT: A 217 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8316 (tp30) REVERT: A 250 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7312 (ttpt) REVERT: A 251 TYR cc_start: 0.8449 (m-10) cc_final: 0.7326 (m-10) REVERT: A 564 GLN cc_start: 0.8918 (tt0) cc_final: 0.8270 (tp-100) REVERT: A 641 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6466 (p-80) REVERT: A 664 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8684 (pt0) REVERT: A 794 HIS cc_start: 0.7669 (m170) cc_final: 0.7081 (t70) REVERT: B 217 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7897 (mp0) REVERT: B 254 GLU cc_start: 0.8071 (tt0) cc_final: 0.7569 (tt0) REVERT: B 298 MET cc_start: 0.8826 (mtp) cc_final: 0.8567 (mtp) REVERT: B 388 ASP cc_start: 0.8800 (t70) cc_final: 0.8420 (t0) REVERT: B 392 ASP cc_start: 0.8607 (m-30) cc_final: 0.8027 (t0) REVERT: B 533 ASP cc_start: 0.8101 (p0) cc_final: 0.7751 (p0) REVERT: B 581 SER cc_start: 0.9257 (m) cc_final: 0.8766 (p) REVERT: B 633 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7454 (p0) REVERT: B 700 THR cc_start: 0.8584 (m) cc_final: 0.8358 (m) REVERT: B 808 TYR cc_start: 0.5864 (t80) cc_final: 0.5285 (t80) REVERT: C 241 ASP cc_start: 0.7737 (t0) cc_final: 0.7374 (t0) REVERT: C 257 GLU cc_start: 0.8303 (tt0) cc_final: 0.8006 (tt0) REVERT: C 737 MET cc_start: 0.8739 (tpp) cc_final: 0.8409 (tpp) REVERT: C 780 LYS cc_start: 0.9120 (mttt) cc_final: 0.8808 (tptt) REVERT: C 786 LEU cc_start: 0.9525 (tp) cc_final: 0.9191 (tp) REVERT: D 163 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8503 (mptt) REVERT: D 392 ASP cc_start: 0.8132 (m-30) cc_final: 0.7920 (m-30) REVERT: D 710 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8414 (mtp85) REVERT: D 794 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7841 (m-70) REVERT: D 827 ASN cc_start: 0.8621 (m-40) cc_final: 0.8079 (m110) REVERT: E 162 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8321 (pttm) REVERT: E 242 MET cc_start: 0.7616 (mmt) cc_final: 0.7216 (mmt) REVERT: E 257 GLU cc_start: 0.8861 (tt0) cc_final: 0.8600 (mm-30) REVERT: E 268 LYS cc_start: 0.7278 (tttt) cc_final: 0.6875 (pttm) REVERT: E 298 MET cc_start: 0.7555 (mtp) cc_final: 0.7261 (mtt) REVERT: E 317 ASP cc_start: 0.8594 (m-30) cc_final: 0.8355 (m-30) REVERT: E 318 GLU cc_start: 0.8809 (mp0) cc_final: 0.8455 (mp0) REVERT: E 359 LEU cc_start: 0.9063 (mp) cc_final: 0.8703 (mp) REVERT: E 406 ASP cc_start: 0.8251 (t0) cc_final: 0.7655 (t70) REVERT: E 567 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7632 (t-90) REVERT: E 707 VAL cc_start: 0.9422 (t) cc_final: 0.9058 (m) REVERT: E 726 GLN cc_start: 0.7581 (mt0) cc_final: 0.7234 (pt0) REVERT: E 745 VAL cc_start: 0.8634 (t) cc_final: 0.8396 (p) REVERT: F 178 ASP cc_start: 0.8288 (m-30) cc_final: 0.7910 (p0) REVERT: F 217 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7668 (mt-10) REVERT: F 254 GLU cc_start: 0.5891 (tp30) cc_final: 0.5549 (tp30) REVERT: F 330 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7247 (pt0) REVERT: F 376 LEU cc_start: 0.8284 (mm) cc_final: 0.8083 (pp) REVERT: F 538 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8069 (tm-30) REVERT: F 582 ASN cc_start: 0.9007 (m-40) cc_final: 0.8750 (m-40) REVERT: F 588 ARG cc_start: 0.8666 (mmt90) cc_final: 0.8165 (ptp-170) REVERT: F 629 MET cc_start: 0.8336 (ptm) cc_final: 0.7955 (ptm) REVERT: F 821 ILE cc_start: 0.8981 (mt) cc_final: 0.8702 (mt) outliers start: 84 outliers final: 72 residues processed: 445 average time/residue: 0.4178 time to fit residues: 299.2279 Evaluate side-chains 441 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 364 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN E 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29298 Z= 0.235 Angle : 0.612 18.661 39598 Z= 0.298 Chirality : 0.043 0.218 4479 Planarity : 0.004 0.055 5170 Dihedral : 8.271 67.291 4209 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.99 % Allowed : 15.86 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3563 helix: 0.96 (0.12), residues: 1942 sheet: -1.98 (0.25), residues: 383 loop : -1.12 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 543 HIS 0.006 0.001 HIS E 568 PHE 0.027 0.002 PHE D 276 TYR 0.026 0.001 TYR A 656 ARG 0.005 0.000 ARG E 756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 378 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8219 (tp30) cc_final: 0.7902 (tp30) REVERT: A 217 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8255 (mm-30) REVERT: A 250 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7263 (ttpt) REVERT: A 251 TYR cc_start: 0.8457 (m-10) cc_final: 0.7330 (m-10) REVERT: A 403 MET cc_start: 0.7338 (ttm) cc_final: 0.6930 (mmp) REVERT: A 564 GLN cc_start: 0.8931 (tt0) cc_final: 0.8275 (tp-100) REVERT: A 585 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: A 623 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: A 641 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6464 (p-80) REVERT: A 664 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8719 (pt0) REVERT: A 738 LYS cc_start: 0.7450 (tttt) cc_final: 0.6875 (pttm) REVERT: A 794 HIS cc_start: 0.7662 (m170) cc_final: 0.7075 (t70) REVERT: B 200 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 254 GLU cc_start: 0.8096 (tt0) cc_final: 0.7563 (tt0) REVERT: B 298 MET cc_start: 0.8858 (mtp) cc_final: 0.8586 (mtp) REVERT: B 388 ASP cc_start: 0.8817 (t70) cc_final: 0.8276 (t0) REVERT: B 392 ASP cc_start: 0.8611 (m-30) cc_final: 0.8035 (t0) REVERT: B 533 ASP cc_start: 0.8107 (p0) cc_final: 0.7760 (p0) REVERT: B 581 SER cc_start: 0.9270 (m) cc_final: 0.8755 (p) REVERT: B 633 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7276 (p0) REVERT: B 700 THR cc_start: 0.8580 (m) cc_final: 0.8357 (m) REVERT: B 808 TYR cc_start: 0.5919 (t80) cc_final: 0.5317 (t80) REVERT: C 241 ASP cc_start: 0.7712 (t0) cc_final: 0.7366 (t0) REVERT: C 257 GLU cc_start: 0.8306 (tt0) cc_final: 0.8018 (tt0) REVERT: C 664 GLU cc_start: 0.7087 (pt0) cc_final: 0.6834 (pt0) REVERT: C 737 MET cc_start: 0.8655 (tpp) cc_final: 0.8386 (tpp) REVERT: C 780 LYS cc_start: 0.9117 (mttt) cc_final: 0.8810 (tptt) REVERT: C 786 LEU cc_start: 0.9546 (tp) cc_final: 0.9226 (tp) REVERT: D 163 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8485 (mptt) REVERT: D 392 ASP cc_start: 0.8165 (m-30) cc_final: 0.7953 (m-30) REVERT: D 551 MET cc_start: 0.6998 (mmm) cc_final: 0.6436 (mmm) REVERT: D 710 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8436 (mtp85) REVERT: D 794 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7823 (m-70) REVERT: D 827 ASN cc_start: 0.8615 (m-40) cc_final: 0.8071 (m110) REVERT: E 162 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8339 (pttm) REVERT: E 242 MET cc_start: 0.7600 (mmt) cc_final: 0.7191 (mmt) REVERT: E 257 GLU cc_start: 0.8861 (tt0) cc_final: 0.8603 (mm-30) REVERT: E 268 LYS cc_start: 0.7271 (tttt) cc_final: 0.6874 (pttm) REVERT: E 298 MET cc_start: 0.7508 (mtp) cc_final: 0.7209 (mtt) REVERT: E 317 ASP cc_start: 0.8606 (m-30) cc_final: 0.8364 (m-30) REVERT: E 318 GLU cc_start: 0.8807 (mp0) cc_final: 0.8434 (mp0) REVERT: E 359 LEU cc_start: 0.9084 (mp) cc_final: 0.8733 (mp) REVERT: E 567 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7719 (t-90) REVERT: E 633 ASP cc_start: 0.8462 (m-30) cc_final: 0.8158 (m-30) REVERT: E 685 ASP cc_start: 0.8906 (t0) cc_final: 0.8683 (t0) REVERT: E 707 VAL cc_start: 0.9469 (t) cc_final: 0.9098 (m) REVERT: E 726 GLN cc_start: 0.7499 (mt0) cc_final: 0.7220 (pt0) REVERT: E 745 VAL cc_start: 0.8632 (t) cc_final: 0.8408 (p) REVERT: F 178 ASP cc_start: 0.8204 (m-30) cc_final: 0.7887 (p0) REVERT: F 217 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7750 (mt-10) REVERT: F 254 GLU cc_start: 0.5961 (tp30) cc_final: 0.5635 (tp30) REVERT: F 330 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7265 (pt0) REVERT: F 376 LEU cc_start: 0.8297 (mm) cc_final: 0.8095 (pp) REVERT: F 538 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8077 (tm-30) REVERT: F 582 ASN cc_start: 0.9026 (m-40) cc_final: 0.8761 (m-40) REVERT: F 588 ARG cc_start: 0.8689 (mmt90) cc_final: 0.8233 (ptp-170) REVERT: F 629 MET cc_start: 0.8326 (ptm) cc_final: 0.7950 (ptm) REVERT: F 821 ILE cc_start: 0.8965 (mt) cc_final: 0.8679 (mt) REVERT: F 851 ASP cc_start: 0.8646 (t0) cc_final: 0.8328 (t0) outliers start: 90 outliers final: 74 residues processed: 436 average time/residue: 0.3948 time to fit residues: 278.4753 Evaluate side-chains 446 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 365 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 0.0570 chunk 358 optimal weight: 30.0000 chunk 330 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29298 Z= 0.180 Angle : 0.595 20.887 39598 Z= 0.289 Chirality : 0.042 0.216 4479 Planarity : 0.004 0.056 5170 Dihedral : 8.124 67.468 4209 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.73 % Allowed : 16.32 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3563 helix: 1.06 (0.12), residues: 1940 sheet: -1.94 (0.26), residues: 366 loop : -1.09 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 543 HIS 0.006 0.001 HIS E 568 PHE 0.026 0.002 PHE C 729 TYR 0.034 0.001 TYR A 656 ARG 0.005 0.000 ARG E 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 389 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8261 (tp30) cc_final: 0.7952 (tp30) REVERT: A 217 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 250 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7282 (ttpt) REVERT: A 251 TYR cc_start: 0.8443 (m-10) cc_final: 0.7305 (m-10) REVERT: A 403 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6974 (mmp) REVERT: A 564 GLN cc_start: 0.8941 (tt0) cc_final: 0.8289 (tp-100) REVERT: A 585 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: A 641 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6427 (p-80) REVERT: A 794 HIS cc_start: 0.7658 (m170) cc_final: 0.7071 (t70) REVERT: A 842 LYS cc_start: 0.1886 (OUTLIER) cc_final: 0.1675 (ptmt) REVERT: B 200 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 217 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 254 GLU cc_start: 0.8083 (tt0) cc_final: 0.7587 (tt0) REVERT: B 298 MET cc_start: 0.8810 (mtp) cc_final: 0.8548 (mtp) REVERT: B 388 ASP cc_start: 0.8764 (t70) cc_final: 0.8375 (t0) REVERT: B 392 ASP cc_start: 0.8563 (m-30) cc_final: 0.7979 (t0) REVERT: B 533 ASP cc_start: 0.8102 (p0) cc_final: 0.7762 (p0) REVERT: B 581 SER cc_start: 0.9284 (m) cc_final: 0.8818 (p) REVERT: B 633 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 700 THR cc_start: 0.8545 (m) cc_final: 0.8316 (m) REVERT: B 808 TYR cc_start: 0.5926 (t80) cc_final: 0.5496 (t80) REVERT: C 241 ASP cc_start: 0.7642 (t0) cc_final: 0.7302 (t0) REVERT: C 257 GLU cc_start: 0.8310 (tt0) cc_final: 0.8015 (tt0) REVERT: C 780 LYS cc_start: 0.9113 (mttt) cc_final: 0.8806 (tptt) REVERT: C 786 LEU cc_start: 0.9537 (tp) cc_final: 0.9218 (tp) REVERT: D 163 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8462 (mptt) REVERT: D 326 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7225 (p0) REVERT: D 551 MET cc_start: 0.6910 (mmm) cc_final: 0.6437 (mmm) REVERT: D 710 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8448 (mtp85) REVERT: D 794 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7849 (m-70) REVERT: D 827 ASN cc_start: 0.8593 (m-40) cc_final: 0.8024 (m110) REVERT: D 844 ILE cc_start: 0.9089 (mt) cc_final: 0.8832 (mp) REVERT: E 162 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8318 (pttm) REVERT: E 242 MET cc_start: 0.7529 (mmt) cc_final: 0.7119 (mmt) REVERT: E 257 GLU cc_start: 0.8858 (tt0) cc_final: 0.8604 (mm-30) REVERT: E 268 LYS cc_start: 0.7257 (tttt) cc_final: 0.6867 (pttm) REVERT: E 298 MET cc_start: 0.7435 (mtp) cc_final: 0.7139 (mtt) REVERT: E 317 ASP cc_start: 0.8597 (m-30) cc_final: 0.8345 (m-30) REVERT: E 318 GLU cc_start: 0.8803 (mp0) cc_final: 0.8419 (mp0) REVERT: E 359 LEU cc_start: 0.9070 (mp) cc_final: 0.8822 (mp) REVERT: E 567 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: E 581 SER cc_start: 0.9222 (m) cc_final: 0.8882 (p) REVERT: E 685 ASP cc_start: 0.8809 (t0) cc_final: 0.8594 (t0) REVERT: E 707 VAL cc_start: 0.9481 (t) cc_final: 0.9080 (m) REVERT: E 726 GLN cc_start: 0.7539 (mt0) cc_final: 0.7206 (pt0) REVERT: E 745 VAL cc_start: 0.8602 (t) cc_final: 0.8369 (p) REVERT: E 822 GLN cc_start: 0.8541 (tt0) cc_final: 0.8248 (tp40) REVERT: F 178 ASP cc_start: 0.8229 (m-30) cc_final: 0.7890 (p0) REVERT: F 217 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7759 (mt-10) REVERT: F 254 GLU cc_start: 0.5756 (tp30) cc_final: 0.5489 (tp30) REVERT: F 330 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7266 (pt0) REVERT: F 376 LEU cc_start: 0.8261 (mm) cc_final: 0.8052 (pp) REVERT: F 538 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8121 (tm-30) REVERT: F 582 ASN cc_start: 0.9006 (m-40) cc_final: 0.8734 (m-40) REVERT: F 588 ARG cc_start: 0.8684 (mmt90) cc_final: 0.8199 (ptp-170) REVERT: F 629 MET cc_start: 0.8259 (ptm) cc_final: 0.7911 (ptm) REVERT: F 821 ILE cc_start: 0.8975 (mt) cc_final: 0.8692 (mt) outliers start: 82 outliers final: 65 residues processed: 439 average time/residue: 0.4090 time to fit residues: 289.9168 Evaluate side-chains 444 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 370 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 52 optimal weight: 5.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096245 restraints weight = 57534.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098545 restraints weight = 31385.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098978 restraints weight = 21573.387| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29298 Z= 0.178 Angle : 0.594 20.046 39598 Z= 0.289 Chirality : 0.043 0.219 4479 Planarity : 0.004 0.067 5170 Dihedral : 8.004 67.430 4209 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.63 % Allowed : 16.59 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3563 helix: 1.15 (0.12), residues: 1932 sheet: -1.90 (0.26), residues: 370 loop : -1.01 (0.19), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 543 HIS 0.006 0.001 HIS E 568 PHE 0.024 0.002 PHE D 276 TYR 0.031 0.001 TYR A 656 ARG 0.005 0.000 ARG F 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6675.24 seconds wall clock time: 122 minutes 22.82 seconds (7342.82 seconds total)