Starting phenix.real_space_refine on Sun Mar 17 19:15:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvz_26142/03_2024/7tvz_26142_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12124 2.51 5 N 3115 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18659 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6663 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 52, 'TRANS': 797} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6489 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 50, 'TRANS': 774} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 1, 'LMT': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'CLR': 1, 'LMT': 3, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 10.24, per 1000 atoms: 0.55 Number of scatterers: 18659 At special positions: 0 Unit cell: (111.1, 141.9, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3348 8.00 N 3115 7.00 C 12124 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=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 642 " " NAG B1102 " - " ASN B 642 " Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 3.7 seconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 17 sheets defined 43.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.562A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.911A pdb=" N GLU A 168 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 328 through 346 removed outlier: 4.182A pdb=" N LEU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 380 through 398 Proline residue: A 391 - end of helix removed outlier: 5.334A pdb=" N LEU A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 430 removed outlier: 3.768A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 437 through 454 Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 489 through 506 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 546 Processing helix chain 'A' and resid 570 through 593 removed outlier: 4.016A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 623 removed outlier: 3.702A pdb=" N GLY A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 668 through 689 removed outlier: 3.574A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 703 through 718 Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 761 through 775 removed outlier: 4.911A pdb=" N ILE A 774 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU A 775 " --> pdb=" O GLY A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.177A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.869A pdb=" N PHE A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 removed outlier: 3.536A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 856 through 871 Proline residue: A 860 - end of helix Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.706A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLU B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 152 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 157 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 196 through 199 No H-bonds generated for 'chain 'B' and resid 196 through 199' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.791A pdb=" N LEU B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Proline residue: B 337 - end of helix Processing helix chain 'B' and resid 380 through 400 Proline residue: B 391 - end of helix removed outlier: 5.327A pdb=" N LEU B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 430 removed outlier: 3.684A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.549A pdb=" N PHE B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 489 through 507 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 518 through 546 Processing helix chain 'B' and resid 571 through 593 removed outlier: 3.903A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 623 removed outlier: 3.612A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 609 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL B 610 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 668 through 689 removed outlier: 3.573A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 703 through 719 Processing helix chain 'B' and resid 728 through 737 Processing helix chain 'B' and resid 761 through 775 removed outlier: 4.880A pdb=" N ILE B 774 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.345A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.861A pdb=" N PHE B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 812 removed outlier: 3.573A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 826 No H-bonds generated for 'chain 'B' and resid 823 through 826' Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.514A pdb=" N LEU B 835 " --> pdb=" O TRP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 872 Proline residue: B 860 - end of helix Proline residue: B 868 - end of helix removed outlier: 3.604A pdb=" N VAL B 872 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 880 through 886 Processing helix chain 'E' and resid 14 through 20 removed outlier: 4.520A pdb=" N GLU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 188 through 198 removed outlier: 4.239A pdb=" N LYS E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 4.117A pdb=" N SER E 206 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 226 Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 249 through 257 Processing helix chain 'E' and resid 269 through 282 removed outlier: 3.646A pdb=" N ALA E 272 " --> pdb=" O TRP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 442 through 457 removed outlier: 3.664A pdb=" N GLU E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 73 through 80 removed outlier: 6.858A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 58 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 64 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 228 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 265 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 230 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 267 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 263 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 118 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ARG A 246 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 120 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 Processing sheet with id= C, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.067A pdb=" N GLY A 742 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE A 753 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.080A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 58 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG B 233 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N MET B 66 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU B 228 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ARG B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 12.490A pdb=" N LEU B 230 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N LEU B 265 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N GLY B 232 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL B 267 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B 118 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG B 246 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 120 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= F, first strand: chain 'B' and resid 739 through 742 removed outlier: 5.930A pdb=" N GLY B 742 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE B 753 " --> pdb=" O GLY B 742 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 32 through 34 removed outlier: 8.360A pdb=" N VAL E 33 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR E 135 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU E 119 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN E 133 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR E 117 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR E 135 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 115 " --> pdb=" O THR E 135 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 7 through 12 removed outlier: 7.295A pdb=" N TYR E 44 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N CYS E 10 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE E 42 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE E 12 " --> pdb=" O THR E 40 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR E 40 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 96 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER E 105 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL E 94 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR E 107 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA E 92 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 163 through 169 Processing sheet with id= J, first strand: chain 'E' and resid 286 through 292 removed outlier: 11.582A pdb=" N THR E 328 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR E 330 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 364 " --> pdb=" O HIS E 350 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 303 through 308 removed outlier: 6.981A pdb=" N SER E 392 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU E 306 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 394 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR E 308 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP E 396 " --> pdb=" O TYR E 308 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 419 through 421 Processing sheet with id= M, first strand: chain 'E' and resid 475 through 480 Processing sheet with id= N, first strand: chain 'E' and resid 484 through 486 removed outlier: 6.565A pdb=" N ALA E 584 " --> pdb=" O LEU E 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 576 through 583 removed outlier: 6.469A pdb=" N ALA E 515 " --> pdb=" O LYS E 525 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS E 525 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 590 through 593 Processing sheet with id= Q, first strand: chain 'E' and resid 597 through 599 removed outlier: 8.539A pdb=" N ALA E 598 " --> pdb=" O SER E 681 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR E 683 " --> pdb=" O ALA E 598 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2163 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: 6.30 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5926 1.34 - 1.46: 4194 1.46 - 1.58: 8837 1.58 - 1.70: 7 1.70 - 1.82: 121 Bond restraints: 19085 Sorted by residual: bond pdb=" C15 CLR A1003 " pdb=" C16 CLR A1003 " ideal model delta sigma weight residual 1.541 1.715 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C15 CLR B1104 " pdb=" C16 CLR B1104 " ideal model delta sigma weight residual 1.541 1.714 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 CLR A1003 " pdb=" C9 CLR A1003 " ideal model delta sigma weight residual 1.551 1.390 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C10 CLR B1104 " pdb=" C9 CLR B1104 " ideal model delta sigma weight residual 1.551 1.395 0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" C5 CLR A1003 " pdb=" C6 CLR A1003 " ideal model delta sigma weight residual 1.332 1.472 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 19080 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.85: 531 105.85 - 112.89: 10539 112.89 - 119.93: 6188 119.93 - 126.97: 8424 126.97 - 134.01: 257 Bond angle restraints: 25939 Sorted by residual: angle pdb=" C ARG E 638 " pdb=" N PHE E 639 " pdb=" CA PHE E 639 " ideal model delta sigma weight residual 121.87 127.31 -5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" CB MET E 456 " pdb=" CG MET E 456 " pdb=" SD MET E 456 " ideal model delta sigma weight residual 112.70 121.18 -8.48 3.00e+00 1.11e-01 7.99e+00 angle pdb=" C6 LMT A1004 " pdb=" C7 LMT A1004 " pdb=" C8 LMT A1004 " ideal model delta sigma weight residual 117.26 108.80 8.46 3.00e+00 1.11e-01 7.95e+00 angle pdb=" C1B LMT A1004 " pdb=" O1B LMT A1004 " pdb=" C4' LMT A1004 " ideal model delta sigma weight residual 117.87 110.00 7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" C6 LMT B1103 " pdb=" C7 LMT B1103 " pdb=" C8 LMT B1103 " ideal model delta sigma weight residual 117.26 109.42 7.84 3.00e+00 1.11e-01 6.83e+00 ... (remaining 25934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 11014 24.18 - 48.37: 632 48.37 - 72.55: 69 72.55 - 96.73: 16 96.73 - 120.92: 12 Dihedral angle restraints: 11743 sinusoidal: 4985 harmonic: 6758 Sorted by residual: dihedral pdb=" C2B LMT B1105 " pdb=" C1B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" C5B LMT B1105 " ideal model delta sinusoidal sigma weight residual -57.12 63.80 -120.92 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C1B LMT B1105 " pdb=" C5B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" C6B LMT B1105 " ideal model delta sinusoidal sigma weight residual 175.31 -63.95 -120.74 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C5B LMT B1105 " pdb=" C1B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" O1B LMT B1105 " ideal model delta sinusoidal sigma weight residual 295.61 176.91 118.70 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 11740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2868 0.090 - 0.181: 160 0.181 - 0.271: 2 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 3036 Sorted by residual: chirality pdb=" C9 CLR A1003 " pdb=" C10 CLR A1003 " pdb=" C11 CLR A1003 " pdb=" C8 CLR A1003 " both_signs ideal model delta sigma weight residual False -2.45 -2.90 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C9 CLR B1104 " pdb=" C10 CLR B1104 " pdb=" C11 CLR B1104 " pdb=" C8 CLR B1104 " both_signs ideal model delta sigma weight residual False -2.45 -2.87 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C14 CLR A1003 " pdb=" C13 CLR A1003 " pdb=" C15 CLR A1003 " pdb=" C8 CLR A1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3033 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 447 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLN A 447 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN A 447 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 448 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 831 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C TRP A 831 " 0.051 2.00e-02 2.50e+03 pdb=" O TRP A 831 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 832 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 638 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ARG E 638 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG E 638 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE E 639 " 0.015 2.00e-02 2.50e+03 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1514 2.74 - 3.28: 17645 3.28 - 3.82: 28444 3.82 - 4.36: 32419 4.36 - 4.90: 58729 Nonbonded interactions: 138751 Sorted by model distance: nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A 303 " pdb=" OE1 GLU A 306 " model vdw 2.220 2.440 nonbonded pdb=" O PRO A 271 " pdb=" OH TYR A 278 " model vdw 2.316 2.440 nonbonded pdb=" O2B LMT B1101 " pdb=" O6' LMT B1101 " model vdw 2.316 2.440 nonbonded pdb=" NE2 GLN E 600 " pdb=" O THR E 657 " model vdw 2.318 2.520 ... (remaining 138746 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 55 through 894) selection = (chain 'B' and (resid 55 through 349 or (resid 350 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 through 894)) } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.210 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 51.480 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.005 0.174 19085 Z= 0.316 Angle : 0.611 8.479 25939 Z= 0.270 Chirality : 0.044 0.451 3036 Planarity : 0.004 0.054 3249 Dihedral : 14.937 120.916 7369 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2322 helix: 1.62 (0.17), residues: 1009 sheet: 0.35 (0.28), residues: 341 loop : -1.34 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 723 HIS 0.003 0.000 HIS E 532 PHE 0.013 0.001 PHE E 79 TYR 0.013 0.001 TYR B 519 ARG 0.004 0.000 ARG E 427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9103 (m) cc_final: 0.8693 (p) REVERT: A 72 GLU cc_start: 0.7073 (pp20) cc_final: 0.6597 (pp20) REVERT: A 73 LEU cc_start: 0.8320 (mp) cc_final: 0.7988 (mp) REVERT: A 803 ILE cc_start: 0.7972 (mm) cc_final: 0.7393 (mt) REVERT: E 157 GLU cc_start: 0.8358 (tp30) cc_final: 0.8108 (tp30) REVERT: E 309 ASN cc_start: 0.8052 (t0) cc_final: 0.7834 (t0) REVERT: E 643 TRP cc_start: 0.7985 (m100) cc_final: 0.7779 (m100) REVERT: E 674 GLN cc_start: 0.8665 (mp10) cc_final: 0.8093 (mt0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3251 time to fit residues: 189.5169 Evaluate side-chains 181 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 521 GLN A 547 HIS A 651 HIS A 683 GLN A 752 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS E 64 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19085 Z= 0.412 Angle : 0.707 10.466 25939 Z= 0.343 Chirality : 0.046 0.247 3036 Planarity : 0.006 0.056 3249 Dihedral : 8.403 95.230 2991 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.35 % Allowed : 10.36 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2322 helix: 1.13 (0.17), residues: 1002 sheet: 0.37 (0.29), residues: 339 loop : -1.34 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 333 HIS 0.008 0.001 HIS E 632 PHE 0.023 0.002 PHE A 114 TYR 0.025 0.002 TYR A 824 ARG 0.009 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7442 (ttp) cc_final: 0.7131 (ttt) REVERT: A 72 GLU cc_start: 0.7203 (pp20) cc_final: 0.6567 (pp20) REVERT: A 238 GLU cc_start: 0.7904 (mp0) cc_final: 0.7695 (mp0) REVERT: A 641 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8362 (m) REVERT: A 803 ILE cc_start: 0.8305 (mm) cc_final: 0.7728 (mt) REVERT: A 869 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 218 GLU cc_start: 0.7846 (tt0) cc_final: 0.7251 (pt0) REVERT: E 81 ILE cc_start: 0.8857 (mp) cc_final: 0.8566 (mt) REVERT: E 157 GLU cc_start: 0.8666 (tp30) cc_final: 0.8395 (tp30) REVERT: E 308 TYR cc_start: 0.8554 (m-80) cc_final: 0.8083 (m-10) REVERT: E 309 ASN cc_start: 0.8209 (t0) cc_final: 0.7926 (m-40) REVERT: E 310 GLU cc_start: 0.7984 (tp30) cc_final: 0.7764 (tp30) REVERT: E 674 GLN cc_start: 0.9026 (mp10) cc_final: 0.8201 (mt0) outliers start: 47 outliers final: 29 residues processed: 223 average time/residue: 0.3147 time to fit residues: 107.7145 Evaluate side-chains 194 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19085 Z= 0.231 Angle : 0.576 9.141 25939 Z= 0.275 Chirality : 0.041 0.199 3036 Planarity : 0.005 0.056 3249 Dihedral : 7.068 73.774 2991 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.10 % Allowed : 12.91 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.17), residues: 2322 helix: 1.30 (0.17), residues: 1002 sheet: 0.29 (0.28), residues: 349 loop : -1.31 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 831 HIS 0.005 0.001 HIS B 98 PHE 0.018 0.001 PHE A 471 TYR 0.016 0.002 TYR A 824 ARG 0.003 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7477 (ttp) cc_final: 0.7143 (ttt) REVERT: B 186 GLN cc_start: 0.6057 (mm-40) cc_final: 0.5476 (tp40) REVERT: B 775 LEU cc_start: 0.7869 (mm) cc_final: 0.7654 (mm) REVERT: E 81 ILE cc_start: 0.8860 (mp) cc_final: 0.8611 (mt) REVERT: E 157 GLU cc_start: 0.8627 (tp30) cc_final: 0.8378 (tp30) REVERT: E 308 TYR cc_start: 0.8509 (m-80) cc_final: 0.8040 (m-10) REVERT: E 309 ASN cc_start: 0.8147 (t0) cc_final: 0.7881 (m-40) REVERT: E 674 GLN cc_start: 0.9044 (mp10) cc_final: 0.8176 (mt0) outliers start: 42 outliers final: 30 residues processed: 207 average time/residue: 0.2825 time to fit residues: 92.2152 Evaluate side-chains 193 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19085 Z= 0.234 Angle : 0.558 9.212 25939 Z= 0.267 Chirality : 0.041 0.175 3036 Planarity : 0.005 0.057 3249 Dihedral : 6.303 59.629 2991 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.90 % Allowed : 14.31 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.17), residues: 2322 helix: 1.28 (0.17), residues: 1010 sheet: 0.35 (0.28), residues: 348 loop : -1.28 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 492 HIS 0.004 0.001 HIS B 98 PHE 0.017 0.001 PHE B 511 TYR 0.023 0.002 TYR A 824 ARG 0.003 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 168 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7511 (mp10) cc_final: 0.7291 (mp-120) REVERT: B 186 GLN cc_start: 0.6118 (mm-40) cc_final: 0.5527 (tp40) REVERT: E 81 ILE cc_start: 0.8883 (mp) cc_final: 0.8634 (mt) REVERT: E 157 GLU cc_start: 0.8671 (tp30) cc_final: 0.8413 (tp30) REVERT: E 308 TYR cc_start: 0.8621 (m-80) cc_final: 0.8047 (m-10) REVERT: E 309 ASN cc_start: 0.8160 (t0) cc_final: 0.7891 (m-40) REVERT: E 347 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7531 (mm-40) outliers start: 58 outliers final: 36 residues processed: 213 average time/residue: 0.2851 time to fit residues: 96.2626 Evaluate side-chains 196 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 202 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19085 Z= 0.221 Angle : 0.549 9.798 25939 Z= 0.263 Chirality : 0.040 0.172 3036 Planarity : 0.004 0.058 3249 Dihedral : 6.064 55.862 2991 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.80 % Allowed : 15.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2322 helix: 1.33 (0.17), residues: 1010 sheet: 0.32 (0.28), residues: 348 loop : -1.25 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 831 HIS 0.004 0.001 HIS B 98 PHE 0.018 0.001 PHE B 511 TYR 0.021 0.001 TYR A 824 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 2.253 Fit side-chains revert: symmetry clash REVERT: B 186 GLN cc_start: 0.5971 (mm-40) cc_final: 0.5499 (tp40) REVERT: E 81 ILE cc_start: 0.8896 (mp) cc_final: 0.8647 (mt) REVERT: E 157 GLU cc_start: 0.8679 (tp30) cc_final: 0.8425 (tp30) REVERT: E 308 TYR cc_start: 0.8638 (m-80) cc_final: 0.8057 (m-10) REVERT: E 309 ASN cc_start: 0.8173 (t0) cc_final: 0.7922 (m-40) REVERT: E 347 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: E 549 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.6528 (m-80) outliers start: 56 outliers final: 43 residues processed: 207 average time/residue: 0.2881 time to fit residues: 95.2169 Evaluate side-chains 200 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19085 Z= 0.146 Angle : 0.515 9.961 25939 Z= 0.245 Chirality : 0.039 0.168 3036 Planarity : 0.004 0.059 3249 Dihedral : 5.767 56.963 2991 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.35 % Allowed : 16.87 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.18), residues: 2322 helix: 1.47 (0.17), residues: 1009 sheet: 0.45 (0.28), residues: 347 loop : -1.16 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 492 HIS 0.004 0.001 HIS E 532 PHE 0.016 0.001 PHE B 511 TYR 0.019 0.001 TYR A 824 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: B 186 GLN cc_start: 0.5805 (mm-40) cc_final: 0.5442 (tp40) REVERT: B 496 TRP cc_start: 0.7219 (m100) cc_final: 0.6847 (m100) REVERT: E 81 ILE cc_start: 0.8871 (mp) cc_final: 0.8618 (mt) REVERT: E 157 GLU cc_start: 0.8620 (tp30) cc_final: 0.8388 (tp30) REVERT: E 308 TYR cc_start: 0.8609 (m-80) cc_final: 0.7990 (m-10) REVERT: E 309 ASN cc_start: 0.8125 (t0) cc_final: 0.7892 (m-40) outliers start: 47 outliers final: 30 residues processed: 207 average time/residue: 0.2766 time to fit residues: 91.4307 Evaluate side-chains 190 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 224 optimal weight: 0.1980 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 703 HIS ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19085 Z= 0.196 Angle : 0.531 10.801 25939 Z= 0.252 Chirality : 0.040 0.167 3036 Planarity : 0.004 0.058 3249 Dihedral : 5.685 58.420 2991 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.45 % Allowed : 17.07 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.18), residues: 2322 helix: 1.47 (0.17), residues: 1007 sheet: 0.36 (0.28), residues: 349 loop : -1.12 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 492 HIS 0.003 0.001 HIS E 220 PHE 0.021 0.001 PHE B 511 TYR 0.019 0.001 TYR A 824 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 2.265 Fit side-chains revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7675 (mp10) cc_final: 0.7252 (mp10) REVERT: B 142 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: E 81 ILE cc_start: 0.8880 (mp) cc_final: 0.8639 (mt) REVERT: E 157 GLU cc_start: 0.8675 (tp30) cc_final: 0.8424 (tp30) REVERT: E 308 TYR cc_start: 0.8684 (m-80) cc_final: 0.8086 (m-10) REVERT: E 309 ASN cc_start: 0.8174 (t0) cc_final: 0.7883 (m-40) REVERT: E 347 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7527 (mm-40) REVERT: E 549 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6485 (m-80) outliers start: 49 outliers final: 32 residues processed: 203 average time/residue: 0.2756 time to fit residues: 89.9520 Evaluate side-chains 194 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 111 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 521 GLN ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19085 Z= 0.137 Angle : 0.515 10.534 25939 Z= 0.244 Chirality : 0.039 0.165 3036 Planarity : 0.004 0.058 3249 Dihedral : 5.503 59.614 2991 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.10 % Allowed : 17.77 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.18), residues: 2322 helix: 1.57 (0.17), residues: 1009 sheet: 0.47 (0.28), residues: 349 loop : -1.03 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 831 HIS 0.002 0.000 HIS A 37 PHE 0.019 0.001 PHE B 511 TYR 0.015 0.001 TYR A 824 ARG 0.005 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7816 (mp10) cc_final: 0.7535 (mp10) REVERT: B 142 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 496 TRP cc_start: 0.7050 (m100) cc_final: 0.6698 (m100) REVERT: E 81 ILE cc_start: 0.8883 (mp) cc_final: 0.8633 (mt) REVERT: E 157 GLU cc_start: 0.8629 (tp30) cc_final: 0.8372 (tp30) REVERT: E 308 TYR cc_start: 0.8613 (m-80) cc_final: 0.8070 (m-10) REVERT: E 309 ASN cc_start: 0.8122 (t0) cc_final: 0.7847 (m-40) REVERT: E 347 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7446 (mm-40) REVERT: E 547 LEU cc_start: 0.8297 (tp) cc_final: 0.7956 (tt) REVERT: E 549 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6387 (m-80) outliers start: 42 outliers final: 31 residues processed: 211 average time/residue: 0.2748 time to fit residues: 93.2064 Evaluate side-chains 203 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 164 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 457 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19085 Z= 0.285 Angle : 0.581 9.169 25939 Z= 0.280 Chirality : 0.041 0.168 3036 Planarity : 0.005 0.056 3249 Dihedral : 5.682 59.817 2991 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.40 % Allowed : 17.67 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.18), residues: 2322 helix: 1.43 (0.17), residues: 1008 sheet: 0.36 (0.28), residues: 349 loop : -1.14 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 333 HIS 0.004 0.001 HIS E 220 PHE 0.032 0.002 PHE A 294 TYR 0.018 0.002 TYR A 824 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7837 (mp10) cc_final: 0.7578 (mp10) REVERT: B 142 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: B 496 TRP cc_start: 0.7033 (m100) cc_final: 0.6662 (m100) REVERT: E 81 ILE cc_start: 0.8909 (mp) cc_final: 0.8664 (mt) REVERT: E 157 GLU cc_start: 0.8717 (tp30) cc_final: 0.8472 (tp30) REVERT: E 308 TYR cc_start: 0.8754 (m-80) cc_final: 0.8266 (m-10) REVERT: E 309 ASN cc_start: 0.8181 (t0) cc_final: 0.7862 (m-40) REVERT: E 347 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: E 549 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6535 (m-80) outliers start: 48 outliers final: 35 residues processed: 203 average time/residue: 0.2643 time to fit residues: 86.6994 Evaluate side-chains 195 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 142 optimal weight: 0.0020 chunk 113 optimal weight: 0.3980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 457 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19085 Z= 0.149 Angle : 0.529 10.793 25939 Z= 0.251 Chirality : 0.039 0.181 3036 Planarity : 0.004 0.063 3249 Dihedral : 5.455 59.664 2991 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 18.77 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.18), residues: 2322 helix: 1.55 (0.17), residues: 1008 sheet: 0.49 (0.28), residues: 349 loop : -1.07 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 75 HIS 0.002 0.000 HIS E 220 PHE 0.022 0.001 PHE A 294 TYR 0.018 0.001 TYR A 824 ARG 0.002 0.000 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: B 496 TRP cc_start: 0.7097 (m100) cc_final: 0.6692 (m100) REVERT: E 81 ILE cc_start: 0.8894 (mp) cc_final: 0.8651 (mt) REVERT: E 157 GLU cc_start: 0.8648 (tp30) cc_final: 0.8416 (tp30) REVERT: E 308 TYR cc_start: 0.8651 (m-80) cc_final: 0.8127 (m-10) REVERT: E 309 ASN cc_start: 0.8152 (t0) cc_final: 0.7862 (m-40) REVERT: E 547 LEU cc_start: 0.8318 (tp) cc_final: 0.7978 (tt) REVERT: E 549 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: E 648 MET cc_start: 0.7564 (tmm) cc_final: 0.7091 (tmm) outliers start: 34 outliers final: 29 residues processed: 192 average time/residue: 0.2729 time to fit residues: 84.2121 Evaluate side-chains 191 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 670 CYS Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 457 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123312 restraints weight = 29880.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124818 restraints weight = 34392.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123426 restraints weight = 20664.787| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19085 Z= 0.187 Angle : 0.541 9.406 25939 Z= 0.256 Chirality : 0.039 0.163 3036 Planarity : 0.004 0.058 3249 Dihedral : 5.428 59.771 2991 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.60 % Allowed : 19.02 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.18), residues: 2322 helix: 1.56 (0.17), residues: 1006 sheet: 0.46 (0.28), residues: 349 loop : -1.06 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 492 HIS 0.003 0.001 HIS E 220 PHE 0.023 0.001 PHE A 294 TYR 0.017 0.001 TYR A 824 ARG 0.004 0.000 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.62 seconds wall clock time: 60 minutes 48.59 seconds (3648.59 seconds total)