Starting phenix.real_space_refine on Wed May 21 06:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.map" model { file = "/net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p30_17381/05_2025/8p30_17381.cif" } resolution = 3.29 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 124 5.16 5 Cl 2 4.86 5 C 13670 2.51 5 N 3366 2.21 5 O 3910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21074 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5913 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 35, 'TRANS': 712} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4404 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 552} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 4, 'NDG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, G, H Time building chain proxies: 20.03, per 1000 atoms: 0.95 Number of scatterers: 21074 At special positions: 0 Unit cell: (148.334, 100.967, 175.757, 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) Zn 2 29.99 Cl 2 17.00 S 124 16.00 O 3910 8.00 N 3366 7.00 C 13670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 7 " " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " MAN E 4 " - " MAN E 6 " " BMA G 3 " - " MAN G 4 " " MAN G 4 " - " MAN G 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 546 " " NAG B 903 " - " ASN B 103 " " NAG B 904 " - " ASN B 322 " " NAG B 905 " - " ASN B 432 " " NAG B 906 " - " ASN B 546 " " NAG C 701 " - " ASN C 131 " " NAG C 702 " - " ASN C 357 " " NAG D 701 " - " ASN D 131 " " NAG D 702 " - " ASN D 357 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN B 690 " " NAG H 1 " - " ASN B 90 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 374 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 378 " 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4964 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 12 sheets defined 72.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.651A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.514A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.715A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.970A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.529A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.203A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 306 through 318 removed outlier: 3.825A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.283A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.787A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.836A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.807A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.740A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.674A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.517A pdb=" N ILE A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 768 Processing helix chain 'B' and resid 22 through 53 removed outlier: 3.650A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.512A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.714A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 250 removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.528A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.202A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 306 through 318 removed outlier: 3.824A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.282A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.787A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 431 through 465 removed outlier: 3.836A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.808A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 522 " --> pdb=" O ARG B 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.741A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.674A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.517A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 768 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.580A pdb=" N VAL C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.845A pdb=" N TYR C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Proline residue: C 46 - end of helix removed outlier: 3.721A pdb=" N VAL C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.579A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.943A pdb=" N SER C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 85 through 115 removed outlier: 3.602A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 167 through 188 removed outlier: 3.517A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.649A pdb=" N TYR C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 219 through 229 removed outlier: 3.900A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.740A pdb=" N TRP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.661A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.550A pdb=" N HIS C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.744A pdb=" N TYR C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.584A pdb=" N TRP C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 429 through 445 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.814A pdb=" N MET C 450 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.839A pdb=" N TRP C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 485 through 498 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 552 through 582 removed outlier: 3.640A pdb=" N LEU C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Proline residue: C 571 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.581A pdb=" N VAL D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.845A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Proline residue: D 46 - end of helix removed outlier: 3.720A pdb=" N VAL D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 70 removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.943A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 3.601A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 167 through 188 removed outlier: 3.517A pdb=" N GLY D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.647A pdb=" N TYR D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 219 through 229 removed outlier: 3.901A pdb=" N GLY D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.740A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.660A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 322 removed outlier: 3.550A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.745A pdb=" N TYR D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 Processing helix chain 'D' and resid 372 through 384 Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.584A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Proline residue: D 417 - end of helix Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 429 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.812A pdb=" N MET D 450 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.840A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 482 Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 511 through 532 Processing helix chain 'D' and resid 552 through 582 removed outlier: 3.640A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Proline residue: D 571 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 removed outlier: 6.781A pdb=" N ASP A 693 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.031A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 670 through 673 removed outlier: 6.781A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AB2, first strand: chain 'C' and resid 535 through 540 Processing sheet with id=AB3, first strand: chain 'D' and resid 535 through 540 1295 hydrogen bonds defined for protein. 3783 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: 6.88 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4750 1.33 - 1.45: 5022 1.45 - 1.57: 11660 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21636 Sorted by residual: bond pdb=" C YCP D 703 " pdb=" OXT YCP D 703 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C YCP C 703 " pdb=" OXT YCP C 703 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sigma weight residual 1.392 1.430 -0.038 2.00e-02 2.50e+03 3.53e+00 ... (remaining 21631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28924 1.74 - 3.47: 470 3.47 - 5.21: 84 5.21 - 6.95: 28 6.95 - 8.68: 6 Bond angle restraints: 29512 Sorted by residual: angle pdb=" CA PRO C 353 " pdb=" N PRO C 353 " pdb=" CD PRO C 353 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" CA PRO D 353 " pdb=" N PRO D 353 " pdb=" CD PRO D 353 " ideal model delta sigma weight residual 112.00 104.11 7.89 1.40e+00 5.10e-01 3.17e+01 angle pdb=" CA YCP D 703 " pdb=" C YCP D 703 " pdb=" OXT YCP D 703 " ideal model delta sigma weight residual 120.80 112.55 8.25 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA YCP C 703 " pdb=" C YCP C 703 " pdb=" OXT YCP C 703 " ideal model delta sigma weight residual 120.80 112.59 8.21 1.70e+00 3.46e-01 2.33e+01 angle pdb=" CA GLY B 352 " pdb=" C GLY B 352 " pdb=" O GLY B 352 " ideal model delta sigma weight residual 122.37 120.24 2.13 7.30e-01 1.88e+00 8.49e+00 ... (remaining 29507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 12353 23.80 - 47.60: 509 47.60 - 71.39: 80 71.39 - 95.19: 32 95.19 - 118.99: 16 Dihedral angle restraints: 12990 sinusoidal: 5254 harmonic: 7736 Sorted by residual: dihedral pdb=" CA ASN B 718 " pdb=" C ASN B 718 " pdb=" N ASP B 719 " pdb=" CA ASP B 719 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN A 718 " pdb=" C ASN A 718 " pdb=" N ASP A 719 " pdb=" CA ASP A 719 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C2 MAN E 4 " pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " pdb=" C5 MAN E 4 " ideal model delta sinusoidal sigma weight residual -57.62 61.37 -118.99 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 12987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2830 0.055 - 0.111: 487 0.111 - 0.166: 47 0.166 - 0.222: 2 0.222 - 0.277: 8 Chirality restraints: 3374 Sorted by residual: chirality pdb=" C4 NDG B 902 " pdb=" C3 NDG B 902 " pdb=" C5 NDG B 902 " pdb=" O4 NDG B 902 " both_signs ideal model delta sigma weight residual False -2.30 -2.58 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NDG A 902 " pdb=" C3 NDG A 902 " pdb=" C5 NDG A 902 " pdb=" O4 NDG A 902 " both_signs ideal model delta sigma weight residual False -2.30 -2.57 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3371 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 352 " -0.091 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO C 353 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 353 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 353 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 352 " 0.091 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO D 353 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO D 353 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 353 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 396 " -0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE C 396 " 0.085 2.00e-02 2.50e+03 pdb=" O PHE C 396 " -0.031 2.00e-02 2.50e+03 pdb=" N PHE C 397 " -0.029 2.00e-02 2.50e+03 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 158 2.60 - 3.18: 18635 3.18 - 3.75: 33729 3.75 - 4.33: 45305 4.33 - 4.90: 75541 Nonbonded interactions: 173368 Sorted by model distance: nonbonded pdb=" SG CYS C 126 " pdb=" SG CYS C 139 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS D 126 " pdb=" SG CYS D 139 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 309 " pdb=" SG CYS C 358 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 309 " pdb=" SG CYS D 358 " model vdw 2.032 3.760 nonbonded pdb=" OE2 GLU B 402 " pdb="ZN ZN B 901 " model vdw 2.050 2.230 ... (remaining 173363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 60.800 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.004 0.067 21678 Z= 0.170 Angle : 0.603 8.682 29614 Z= 0.302 Chirality : 0.043 0.277 3374 Planarity : 0.005 0.133 3684 Dihedral : 14.221 118.989 8008 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.23 % Allowed : 9.19 % Favored : 90.58 % 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: 1.31 (0.17), residues: 2634 helix: 1.71 (0.13), residues: 1684 sheet: 0.55 (0.69), residues: 54 loop : -0.71 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE C 460 TYR 0.010 0.001 TYR C 348 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 16) link_NAG-ASN : angle 1.98713 ( 48) link_ALPHA1-6 : bond 0.00501 ( 4) link_ALPHA1-6 : angle 1.77722 ( 12) link_BETA1-4 : bond 0.01050 ( 6) link_BETA1-4 : angle 3.63799 ( 18) link_ALPHA1-3 : bond 0.00407 ( 4) link_ALPHA1-3 : angle 3.12896 ( 12) hydrogen bonds : bond 0.13839 ( 1287) hydrogen bonds : angle 5.58948 ( 3783) metal coordination : bond 0.00150 ( 4) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.63967 ( 12) covalent geometry : bond 0.00351 (21636) covalent geometry : angle 0.58752 (29512) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 445 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8119 (p) cc_final: 0.7904 (p) REVERT: A 151 ILE cc_start: 0.8719 (mt) cc_final: 0.8501 (mm) REVERT: B 107 VAL cc_start: 0.8066 (p) cc_final: 0.7851 (p) REVERT: B 376 MET cc_start: 0.8885 (ttm) cc_final: 0.8594 (ttt) REVERT: B 401 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (t70) REVERT: C 52 ILE cc_start: 0.8479 (mt) cc_final: 0.8043 (mm) REVERT: C 69 MET cc_start: 0.8596 (mmp) cc_final: 0.8107 (mmp) REVERT: C 198 PHE cc_start: 0.8254 (t80) cc_final: 0.7968 (t80) REVERT: C 202 LEU cc_start: 0.8576 (tp) cc_final: 0.8239 (tp) REVERT: C 241 TRP cc_start: 0.7707 (m100) cc_final: 0.7249 (m-10) REVERT: C 391 TRP cc_start: 0.8031 (m100) cc_final: 0.7551 (m100) REVERT: C 414 ILE cc_start: 0.8130 (mt) cc_final: 0.7478 (mt) REVERT: C 476 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 508 MET cc_start: 0.8415 (mmm) cc_final: 0.8053 (mtt) REVERT: D 69 MET cc_start: 0.8672 (mmp) cc_final: 0.8174 (mmp) REVERT: D 202 LEU cc_start: 0.8556 (tp) cc_final: 0.8103 (tp) REVERT: D 241 TRP cc_start: 0.7728 (m100) cc_final: 0.7283 (m-10) REVERT: D 391 TRP cc_start: 0.8063 (m100) cc_final: 0.7635 (m100) REVERT: D 437 VAL cc_start: 0.9129 (t) cc_final: 0.8900 (p) REVERT: D 508 MET cc_start: 0.8391 (mmm) cc_final: 0.8053 (mtt) outliers start: 5 outliers final: 0 residues processed: 448 average time/residue: 0.3198 time to fit residues: 220.7101 Evaluate side-chains 242 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 401 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 237 optimal weight: 0.0970 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 96 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 24 GLN B 96 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 410 ASN C 545 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 410 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087588 restraints weight = 42051.226| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.94 r_work: 0.3039 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21678 Z= 0.151 Angle : 0.602 13.847 29614 Z= 0.293 Chirality : 0.042 0.268 3374 Planarity : 0.004 0.078 3684 Dihedral : 10.494 110.177 3508 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.87 % Allowed : 12.22 % Favored : 85.91 % 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: 1.61 (0.17), residues: 2634 helix: 1.87 (0.13), residues: 1702 sheet: 0.34 (0.54), residues: 82 loop : -0.48 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 48 HIS 0.009 0.001 HIS A 34 PHE 0.025 0.002 PHE C 262 TYR 0.012 0.001 TYR B 516 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 16) link_NAG-ASN : angle 1.89263 ( 48) link_ALPHA1-6 : bond 0.00217 ( 4) link_ALPHA1-6 : angle 2.10615 ( 12) link_BETA1-4 : bond 0.00703 ( 6) link_BETA1-4 : angle 3.07454 ( 18) link_ALPHA1-3 : bond 0.00493 ( 4) link_ALPHA1-3 : angle 2.89251 ( 12) hydrogen bonds : bond 0.04733 ( 1287) hydrogen bonds : angle 4.19543 ( 3783) metal coordination : bond 0.00145 ( 4) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.29972 ( 12) covalent geometry : bond 0.00332 (21636) covalent geometry : angle 0.58899 (29512) Misc. bond : bond 0.00136 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TRP cc_start: 0.8042 (m100) cc_final: 0.7694 (m100) REVERT: A 462 MET cc_start: 0.8427 (mtt) cc_final: 0.7702 (mtm) REVERT: B 323 MET cc_start: 0.8293 (mmm) cc_final: 0.7984 (mmm) REVERT: B 376 MET cc_start: 0.9221 (ttm) cc_final: 0.8884 (ttt) REVERT: B 401 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8235 (t70) REVERT: B 462 MET cc_start: 0.8405 (mtt) cc_final: 0.7666 (mtm) REVERT: C 50 MET cc_start: 0.8893 (tpp) cc_final: 0.8524 (mmp) REVERT: C 68 ARG cc_start: 0.8568 (tpt90) cc_final: 0.8039 (tpt90) REVERT: C 69 MET cc_start: 0.8353 (mmp) cc_final: 0.8113 (mmp) REVERT: C 241 TRP cc_start: 0.7733 (m100) cc_final: 0.7449 (m-10) REVERT: C 385 MET cc_start: 0.7767 (mmt) cc_final: 0.7340 (mmt) REVERT: C 509 TRP cc_start: 0.7967 (m-10) cc_final: 0.7755 (m-90) REVERT: C 512 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8138 (m) REVERT: D 50 MET cc_start: 0.8876 (tpp) cc_final: 0.8526 (mmp) REVERT: D 68 ARG cc_start: 0.8562 (tpt90) cc_final: 0.8002 (tpt90) REVERT: D 69 MET cc_start: 0.8353 (mmp) cc_final: 0.8087 (mmp) REVERT: D 241 TRP cc_start: 0.7600 (m100) cc_final: 0.7384 (m-10) REVERT: D 437 VAL cc_start: 0.9132 (t) cc_final: 0.8901 (p) REVERT: D 512 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8178 (m) REVERT: D 545 GLN cc_start: 0.7437 (mt0) cc_final: 0.7059 (mt0) outliers start: 40 outliers final: 14 residues processed: 271 average time/residue: 0.3236 time to fit residues: 137.8604 Evaluate side-chains 229 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 242 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088346 restraints weight = 41392.176| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.00 r_work: 0.3038 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21678 Z= 0.126 Angle : 0.581 12.688 29614 Z= 0.279 Chirality : 0.042 0.272 3374 Planarity : 0.004 0.060 3684 Dihedral : 9.492 107.125 3508 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.54 % Allowed : 12.78 % Favored : 85.68 % 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: 1.67 (0.17), residues: 2634 helix: 1.88 (0.13), residues: 1716 sheet: 0.33 (0.54), residues: 82 loop : -0.40 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 48 HIS 0.008 0.001 HIS B 34 PHE 0.024 0.001 PHE B 40 TYR 0.012 0.001 TYR A 516 ARG 0.003 0.000 ARG B 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 16) link_NAG-ASN : angle 1.82582 ( 48) link_ALPHA1-6 : bond 0.00636 ( 4) link_ALPHA1-6 : angle 2.04991 ( 12) link_BETA1-4 : bond 0.01236 ( 6) link_BETA1-4 : angle 2.94896 ( 18) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 2.71643 ( 12) hydrogen bonds : bond 0.04213 ( 1287) hydrogen bonds : angle 3.97713 ( 3783) metal coordination : bond 0.00094 ( 4) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.33633 ( 12) covalent geometry : bond 0.00274 (21636) covalent geometry : angle 0.56866 (29512) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7939 (mtp) cc_final: 0.7656 (mtp) REVERT: B 323 MET cc_start: 0.8191 (mmm) cc_final: 0.7845 (mmm) REVERT: B 376 MET cc_start: 0.9286 (ttm) cc_final: 0.8957 (ttt) REVERT: B 401 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8184 (t70) REVERT: C 33 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7734 (p90) REVERT: C 50 MET cc_start: 0.8865 (tpp) cc_final: 0.8337 (mpp) REVERT: C 68 ARG cc_start: 0.8283 (tpt90) cc_final: 0.8015 (tpt90) REVERT: C 241 TRP cc_start: 0.7580 (m100) cc_final: 0.7356 (m-10) REVERT: C 385 MET cc_start: 0.7906 (mmt) cc_final: 0.7512 (mmt) REVERT: C 397 PHE cc_start: 0.7878 (t80) cc_final: 0.7564 (t80) REVERT: C 407 MET cc_start: 0.8427 (tpt) cc_final: 0.7942 (tpt) REVERT: C 489 PHE cc_start: 0.9016 (t80) cc_final: 0.8813 (t80) REVERT: D 33 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7716 (p90) REVERT: D 50 MET cc_start: 0.8941 (tpp) cc_final: 0.8649 (mmp) REVERT: D 68 ARG cc_start: 0.8371 (tpt90) cc_final: 0.8053 (tpt90) REVERT: D 69 MET cc_start: 0.8380 (mmp) cc_final: 0.8139 (mmp) REVERT: D 397 PHE cc_start: 0.7858 (t80) cc_final: 0.7648 (t80) REVERT: D 407 MET cc_start: 0.8453 (tpt) cc_final: 0.7970 (tpt) REVERT: D 437 VAL cc_start: 0.9124 (t) cc_final: 0.8899 (p) REVERT: D 509 TRP cc_start: 0.7592 (m-10) cc_final: 0.6957 (m-90) REVERT: D 545 GLN cc_start: 0.7528 (mt0) cc_final: 0.7186 (mt0) outliers start: 33 outliers final: 16 residues processed: 257 average time/residue: 0.3142 time to fit residues: 125.7282 Evaluate side-chains 225 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 501 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 113 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.084128 restraints weight = 41920.965| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.08 r_work: 0.2958 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21678 Z= 0.171 Angle : 0.590 12.041 29614 Z= 0.286 Chirality : 0.043 0.276 3374 Planarity : 0.004 0.053 3684 Dihedral : 8.738 103.433 3508 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.87 % Allowed : 12.83 % Favored : 85.31 % 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: 1.62 (0.16), residues: 2634 helix: 1.86 (0.13), residues: 1712 sheet: 0.04 (0.50), residues: 86 loop : -0.44 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 48 HIS 0.011 0.001 HIS A 34 PHE 0.027 0.002 PHE B 40 TYR 0.011 0.001 TYR C 60 ARG 0.007 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 16) link_NAG-ASN : angle 1.78703 ( 48) link_ALPHA1-6 : bond 0.00475 ( 4) link_ALPHA1-6 : angle 2.26851 ( 12) link_BETA1-4 : bond 0.00916 ( 6) link_BETA1-4 : angle 2.81626 ( 18) link_ALPHA1-3 : bond 0.00657 ( 4) link_ALPHA1-3 : angle 2.61302 ( 12) hydrogen bonds : bond 0.04133 ( 1287) hydrogen bonds : angle 3.93536 ( 3783) metal coordination : bond 0.00527 ( 4) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.42989 ( 12) covalent geometry : bond 0.00397 (21636) covalent geometry : angle 0.57843 (29512) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.9253 (mt) cc_final: 0.8657 (mt) REVERT: B 376 MET cc_start: 0.9317 (ttm) cc_final: 0.8989 (ttt) REVERT: B 401 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (t70) REVERT: C 33 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7834 (p90) REVERT: C 50 MET cc_start: 0.8902 (tpp) cc_final: 0.8378 (mpp) REVERT: C 68 ARG cc_start: 0.8382 (tpt90) cc_final: 0.7991 (tpt90) REVERT: C 198 PHE cc_start: 0.8389 (t80) cc_final: 0.8142 (t80) REVERT: C 397 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 407 MET cc_start: 0.8462 (tpt) cc_final: 0.8012 (tpt) REVERT: C 410 ASN cc_start: 0.8422 (t0) cc_final: 0.8148 (t0) REVERT: C 414 ILE cc_start: 0.7754 (mt) cc_final: 0.7502 (mt) REVERT: C 509 TRP cc_start: 0.7496 (m-10) cc_final: 0.6986 (m-90) REVERT: D 33 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7835 (p90) REVERT: D 50 MET cc_start: 0.9040 (tpp) cc_final: 0.8780 (mmp) REVERT: D 198 PHE cc_start: 0.8407 (t80) cc_final: 0.8188 (t80) REVERT: D 397 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (t80) REVERT: D 407 MET cc_start: 0.8530 (tpt) cc_final: 0.8084 (tpt) REVERT: D 414 ILE cc_start: 0.7825 (mt) cc_final: 0.7512 (mt) REVERT: D 437 VAL cc_start: 0.9109 (t) cc_final: 0.8873 (p) REVERT: D 509 TRP cc_start: 0.7768 (m-10) cc_final: 0.7202 (m-90) outliers start: 40 outliers final: 23 residues processed: 250 average time/residue: 0.2985 time to fit residues: 117.7470 Evaluate side-chains 229 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 122 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 277 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.132508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.083914 restraints weight = 42029.090| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.97 r_work: 0.2976 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21678 Z= 0.184 Angle : 0.596 11.856 29614 Z= 0.287 Chirality : 0.043 0.273 3374 Planarity : 0.004 0.050 3684 Dihedral : 8.343 100.268 3508 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 13.15 % Favored : 84.56 % 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: 1.61 (0.16), residues: 2634 helix: 1.83 (0.13), residues: 1718 sheet: -0.13 (0.48), residues: 86 loop : -0.35 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 48 HIS 0.005 0.001 HIS B 34 PHE 0.027 0.002 PHE D 96 TYR 0.011 0.001 TYR D 38 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 16) link_NAG-ASN : angle 1.73648 ( 48) link_ALPHA1-6 : bond 0.00455 ( 4) link_ALPHA1-6 : angle 2.22766 ( 12) link_BETA1-4 : bond 0.01080 ( 6) link_BETA1-4 : angle 2.81851 ( 18) link_ALPHA1-3 : bond 0.00567 ( 4) link_ALPHA1-3 : angle 2.49653 ( 12) hydrogen bonds : bond 0.04093 ( 1287) hydrogen bonds : angle 3.92145 ( 3783) metal coordination : bond 0.00325 ( 4) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.43878 ( 12) covalent geometry : bond 0.00428 (21636) covalent geometry : angle 0.58491 (29512) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8957 (mt) cc_final: 0.8755 (mt) REVERT: A 190 MET cc_start: 0.8172 (tmm) cc_final: 0.7875 (tmm) REVERT: A 392 LEU cc_start: 0.9249 (mt) cc_final: 0.8838 (mt) REVERT: B 100 LEU cc_start: 0.8987 (mt) cc_final: 0.8748 (mt) REVERT: B 190 MET cc_start: 0.8231 (tmm) cc_final: 0.7920 (tmm) REVERT: B 376 MET cc_start: 0.9380 (ttm) cc_final: 0.9042 (ttt) REVERT: B 401 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.8014 (t70) REVERT: C 33 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7757 (p90) REVERT: C 50 MET cc_start: 0.8970 (tpp) cc_final: 0.8414 (mpp) REVERT: C 68 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7964 (tpt90) REVERT: C 198 PHE cc_start: 0.8323 (t80) cc_final: 0.8100 (t80) REVERT: C 344 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7990 (p90) REVERT: C 397 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7686 (t80) REVERT: C 407 MET cc_start: 0.8622 (tpt) cc_final: 0.8163 (tpt) REVERT: C 414 ILE cc_start: 0.7827 (mt) cc_final: 0.7608 (mt) REVERT: C 509 TRP cc_start: 0.7691 (m-10) cc_final: 0.7238 (m-90) REVERT: C 516 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8873 (mp) REVERT: D 33 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7743 (p90) REVERT: D 50 MET cc_start: 0.9077 (tpp) cc_final: 0.8800 (mmp) REVERT: D 68 ARG cc_start: 0.8562 (tpt90) cc_final: 0.8297 (tpt90) REVERT: D 84 LEU cc_start: 0.8036 (mm) cc_final: 0.7823 (mp) REVERT: D 198 PHE cc_start: 0.8467 (t80) cc_final: 0.8261 (t80) REVERT: D 344 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8020 (p90) REVERT: D 397 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 407 MET cc_start: 0.8779 (tpt) cc_final: 0.8383 (tpt) REVERT: D 414 ILE cc_start: 0.7854 (mt) cc_final: 0.7629 (mt) REVERT: D 509 TRP cc_start: 0.7865 (m-10) cc_final: 0.7322 (m-90) outliers start: 49 outliers final: 32 residues processed: 248 average time/residue: 0.3136 time to fit residues: 123.8110 Evaluate side-chains 247 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 25 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084676 restraints weight = 41330.675| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.48 r_work: 0.3037 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21678 Z= 0.118 Angle : 0.558 12.167 29614 Z= 0.265 Chirality : 0.041 0.261 3374 Planarity : 0.004 0.049 3684 Dihedral : 7.903 96.740 3508 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 13.76 % Favored : 84.38 % 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: 1.77 (0.16), residues: 2634 helix: 1.96 (0.13), residues: 1718 sheet: -0.08 (0.49), residues: 86 loop : -0.31 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 48 HIS 0.009 0.001 HIS A 34 PHE 0.016 0.001 PHE B 40 TYR 0.013 0.001 TYR D 101 ARG 0.010 0.000 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 16) link_NAG-ASN : angle 1.68071 ( 48) link_ALPHA1-6 : bond 0.00772 ( 4) link_ALPHA1-6 : angle 2.01019 ( 12) link_BETA1-4 : bond 0.01066 ( 6) link_BETA1-4 : angle 2.78131 ( 18) link_ALPHA1-3 : bond 0.00801 ( 4) link_ALPHA1-3 : angle 2.37324 ( 12) hydrogen bonds : bond 0.03771 ( 1287) hydrogen bonds : angle 3.80160 ( 3783) metal coordination : bond 0.00120 ( 4) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.55251 ( 12) covalent geometry : bond 0.00260 (21636) covalent geometry : angle 0.54711 (29512) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 2.506 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: A 100 LEU cc_start: 0.8963 (mt) cc_final: 0.8755 (mt) REVERT: A 190 MET cc_start: 0.8195 (tmm) cc_final: 0.7896 (tmm) REVERT: A 323 MET cc_start: 0.7939 (mmm) cc_final: 0.7520 (mmm) REVERT: A 392 LEU cc_start: 0.9274 (mt) cc_final: 0.8840 (mt) REVERT: B 48 TRP cc_start: 0.8554 (t60) cc_final: 0.7976 (t60) REVERT: B 190 MET cc_start: 0.8196 (tmm) cc_final: 0.7908 (tmm) REVERT: C 33 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8006 (p90) REVERT: C 68 ARG cc_start: 0.8420 (tpt90) cc_final: 0.7978 (tpt90) REVERT: C 84 LEU cc_start: 0.8202 (mm) cc_final: 0.7994 (mp) REVERT: C 198 PHE cc_start: 0.8275 (t80) cc_final: 0.8045 (t80) REVERT: C 397 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7723 (t80) REVERT: C 407 MET cc_start: 0.8683 (tpt) cc_final: 0.8102 (tpt) REVERT: C 414 ILE cc_start: 0.7729 (mt) cc_final: 0.7518 (mt) REVERT: C 509 TRP cc_start: 0.7803 (m-10) cc_final: 0.7409 (m-90) REVERT: C 516 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8861 (mp) REVERT: D 33 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8010 (p90) REVERT: D 50 MET cc_start: 0.9082 (tpp) cc_final: 0.8870 (mmp) REVERT: D 198 PHE cc_start: 0.8430 (t80) cc_final: 0.8230 (t80) REVERT: D 391 TRP cc_start: 0.8533 (m100) cc_final: 0.8172 (m100) REVERT: D 397 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7636 (t80) REVERT: D 414 ILE cc_start: 0.7844 (mt) cc_final: 0.7612 (mt) REVERT: D 509 TRP cc_start: 0.7945 (m-10) cc_final: 0.7418 (m-90) outliers start: 40 outliers final: 22 residues processed: 242 average time/residue: 0.3040 time to fit residues: 117.0525 Evaluate side-chains 231 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 96 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.085220 restraints weight = 41218.538| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.51 r_work: 0.3029 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21678 Z= 0.117 Angle : 0.566 12.132 29614 Z= 0.265 Chirality : 0.041 0.256 3374 Planarity : 0.004 0.047 3684 Dihedral : 7.654 94.296 3506 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.82 % Allowed : 14.13 % Favored : 84.05 % 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: 1.84 (0.17), residues: 2634 helix: 1.98 (0.13), residues: 1722 sheet: -0.06 (0.50), residues: 86 loop : -0.22 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 48 HIS 0.004 0.001 HIS B 34 PHE 0.028 0.001 PHE C 96 TYR 0.019 0.001 TYR C 524 ARG 0.007 0.000 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 16) link_NAG-ASN : angle 1.64532 ( 48) link_ALPHA1-6 : bond 0.00799 ( 4) link_ALPHA1-6 : angle 2.05860 ( 12) link_BETA1-4 : bond 0.01109 ( 6) link_BETA1-4 : angle 2.76724 ( 18) link_ALPHA1-3 : bond 0.00776 ( 4) link_ALPHA1-3 : angle 2.25796 ( 12) hydrogen bonds : bond 0.03707 ( 1287) hydrogen bonds : angle 3.76126 ( 3783) metal coordination : bond 0.00110 ( 4) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.35206 ( 12) covalent geometry : bond 0.00261 (21636) covalent geometry : angle 0.55548 (29512) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8268 (tmm) cc_final: 0.8050 (tmm) REVERT: A 323 MET cc_start: 0.7923 (mmm) cc_final: 0.7448 (mmm) REVERT: A 392 LEU cc_start: 0.9281 (mt) cc_final: 0.8862 (mt) REVERT: B 190 MET cc_start: 0.8292 (tmm) cc_final: 0.8073 (tmm) REVERT: B 360 MET cc_start: 0.7997 (ppp) cc_final: 0.7690 (ppp) REVERT: C 33 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8192 (p90) REVERT: C 68 ARG cc_start: 0.8414 (tpt90) cc_final: 0.8039 (tpt90) REVERT: C 198 PHE cc_start: 0.8313 (t80) cc_final: 0.8101 (t80) REVERT: C 344 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7821 (p90) REVERT: C 391 TRP cc_start: 0.8596 (m100) cc_final: 0.8223 (m100) REVERT: C 397 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7671 (t80) REVERT: C 509 TRP cc_start: 0.7952 (m-10) cc_final: 0.7494 (m-90) REVERT: C 516 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8843 (mp) REVERT: D 33 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8181 (p90) REVERT: D 50 MET cc_start: 0.9140 (tpp) cc_final: 0.8903 (mmp) REVERT: D 198 PHE cc_start: 0.8405 (t80) cc_final: 0.8203 (t80) REVERT: D 344 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7836 (p90) REVERT: D 385 MET cc_start: 0.7540 (mmp) cc_final: 0.7332 (mmp) REVERT: D 391 TRP cc_start: 0.8478 (m100) cc_final: 0.8243 (m100) REVERT: D 397 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7672 (t80) REVERT: D 414 ILE cc_start: 0.7880 (mt) cc_final: 0.7667 (mt) REVERT: D 509 TRP cc_start: 0.7965 (m-10) cc_final: 0.7575 (m-90) outliers start: 39 outliers final: 23 residues processed: 241 average time/residue: 0.3123 time to fit residues: 119.8812 Evaluate side-chains 231 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 187 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 173 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084186 restraints weight = 41330.516| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.52 r_work: 0.3003 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21678 Z= 0.143 Angle : 0.580 11.894 29614 Z= 0.274 Chirality : 0.042 0.254 3374 Planarity : 0.004 0.046 3684 Dihedral : 7.570 90.722 3506 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.59 % Allowed : 14.41 % Favored : 84.00 % 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: 1.84 (0.17), residues: 2634 helix: 2.02 (0.13), residues: 1704 sheet: -0.06 (0.49), residues: 86 loop : -0.25 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 48 HIS 0.006 0.001 HIS B 378 PHE 0.040 0.001 PHE D 262 TYR 0.021 0.001 TYR B 183 ARG 0.006 0.001 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 16) link_NAG-ASN : angle 1.63210 ( 48) link_ALPHA1-6 : bond 0.00773 ( 4) link_ALPHA1-6 : angle 2.18792 ( 12) link_BETA1-4 : bond 0.01050 ( 6) link_BETA1-4 : angle 2.75927 ( 18) link_ALPHA1-3 : bond 0.00708 ( 4) link_ALPHA1-3 : angle 2.19863 ( 12) hydrogen bonds : bond 0.03761 ( 1287) hydrogen bonds : angle 3.82441 ( 3783) metal coordination : bond 0.00130 ( 4) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.36605 ( 12) covalent geometry : bond 0.00332 (21636) covalent geometry : angle 0.57013 (29512) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 2.330 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: A 183 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8659 (t80) REVERT: A 190 MET cc_start: 0.8338 (tmm) cc_final: 0.8129 (tmm) REVERT: A 323 MET cc_start: 0.7946 (mmm) cc_final: 0.7494 (mmm) REVERT: A 392 LEU cc_start: 0.9279 (mt) cc_final: 0.8862 (mt) REVERT: A 509 ASP cc_start: 0.8328 (t0) cc_final: 0.8055 (t0) REVERT: B 183 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8688 (t80) REVERT: B 190 MET cc_start: 0.8354 (tmm) cc_final: 0.8144 (tmm) REVERT: B 509 ASP cc_start: 0.8314 (t0) cc_final: 0.8073 (t0) REVERT: C 33 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8132 (p90) REVERT: C 68 ARG cc_start: 0.8490 (tpt90) cc_final: 0.8112 (tpt90) REVERT: C 198 PHE cc_start: 0.8303 (t80) cc_final: 0.8086 (t80) REVERT: C 344 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7664 (p90) REVERT: C 391 TRP cc_start: 0.8574 (m100) cc_final: 0.8258 (m100) REVERT: C 397 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 407 MET cc_start: 0.8698 (tpt) cc_final: 0.8177 (tpt) REVERT: C 509 TRP cc_start: 0.7974 (m-10) cc_final: 0.7503 (m-90) REVERT: D 33 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8127 (p90) REVERT: D 50 MET cc_start: 0.9153 (tpp) cc_final: 0.8929 (mmp) REVERT: D 344 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7652 (p90) REVERT: D 391 TRP cc_start: 0.8462 (m100) cc_final: 0.8128 (m100) REVERT: D 397 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7692 (t80) REVERT: D 414 ILE cc_start: 0.7895 (mt) cc_final: 0.7685 (mt) REVERT: D 509 TRP cc_start: 0.7981 (m-10) cc_final: 0.7661 (m-90) outliers start: 34 outliers final: 24 residues processed: 236 average time/residue: 0.3137 time to fit residues: 117.7187 Evaluate side-chains 237 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 250 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082095 restraints weight = 41208.853| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.50 r_work: 0.2973 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21678 Z= 0.200 Angle : 0.631 11.789 29614 Z= 0.301 Chirality : 0.044 0.257 3374 Planarity : 0.004 0.046 3684 Dihedral : 7.625 83.547 3506 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.63 % Allowed : 14.55 % Favored : 83.82 % 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: 1.70 (0.16), residues: 2634 helix: 1.89 (0.13), residues: 1712 sheet: -0.15 (0.48), residues: 86 loop : -0.26 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 48 HIS 0.004 0.001 HIS B 378 PHE 0.044 0.002 PHE D 262 TYR 0.023 0.002 TYR D 524 ARG 0.014 0.001 ARG C 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 16) link_NAG-ASN : angle 1.64293 ( 48) link_ALPHA1-6 : bond 0.00696 ( 4) link_ALPHA1-6 : angle 2.41737 ( 12) link_BETA1-4 : bond 0.01037 ( 6) link_BETA1-4 : angle 2.76009 ( 18) link_ALPHA1-3 : bond 0.00575 ( 4) link_ALPHA1-3 : angle 2.18551 ( 12) hydrogen bonds : bond 0.04032 ( 1287) hydrogen bonds : angle 3.90077 ( 3783) metal coordination : bond 0.00268 ( 4) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.43926 ( 12) covalent geometry : bond 0.00471 (21636) covalent geometry : angle 0.62141 (29512) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9061 (t80) cc_final: 0.8846 (t80) REVERT: A 183 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8888 (t80) REVERT: A 323 MET cc_start: 0.7844 (mmm) cc_final: 0.7501 (mmm) REVERT: A 392 LEU cc_start: 0.9240 (mt) cc_final: 0.8811 (mt) REVERT: A 408 MET cc_start: 0.9098 (mmm) cc_final: 0.8863 (mmm) REVERT: B 408 MET cc_start: 0.9095 (mmm) cc_final: 0.8885 (mmm) REVERT: C 33 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8056 (p90) REVERT: C 68 ARG cc_start: 0.8470 (tpt90) cc_final: 0.8090 (tpt90) REVERT: C 198 PHE cc_start: 0.8309 (t80) cc_final: 0.8099 (t80) REVERT: C 344 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7605 (p90) REVERT: C 391 TRP cc_start: 0.8452 (m100) cc_final: 0.8141 (m100) REVERT: C 397 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7613 (t80) REVERT: C 407 MET cc_start: 0.8722 (tpt) cc_final: 0.8278 (tpt) REVERT: C 509 TRP cc_start: 0.7951 (m-10) cc_final: 0.7532 (m-90) REVERT: C 524 TYR cc_start: 0.8391 (t80) cc_final: 0.8112 (t80) REVERT: D 33 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8057 (p90) REVERT: D 50 MET cc_start: 0.9102 (tpp) cc_final: 0.8894 (mmp) REVERT: D 344 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7579 (p90) REVERT: D 391 TRP cc_start: 0.8366 (m100) cc_final: 0.8055 (m100) REVERT: D 397 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7633 (t80) REVERT: D 414 ILE cc_start: 0.7861 (mt) cc_final: 0.7660 (mt) REVERT: D 509 TRP cc_start: 0.7946 (m-10) cc_final: 0.7642 (m-90) outliers start: 35 outliers final: 27 residues processed: 237 average time/residue: 0.2953 time to fit residues: 111.6687 Evaluate side-chains 240 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 246 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 204 optimal weight: 0.0000 chunk 6 optimal weight: 0.0970 chunk 238 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 146 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: C 27 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** D 106 ASN ** 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 = 0.3975 r_free = 0.3975 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086705 restraints weight = 40878.832| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.98 r_work: 0.3009 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21678 Z= 0.125 Angle : 0.594 12.785 29614 Z= 0.278 Chirality : 0.042 0.249 3374 Planarity : 0.004 0.060 3684 Dihedral : 7.078 77.650 3506 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.31 % Allowed : 14.88 % Favored : 83.82 % 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: 1.81 (0.17), residues: 2634 helix: 1.94 (0.13), residues: 1718 sheet: -0.15 (0.49), residues: 86 loop : -0.16 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 48 HIS 0.004 0.001 HIS B 34 PHE 0.042 0.001 PHE D 262 TYR 0.030 0.001 TYR B 183 ARG 0.013 0.001 ARG C 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 16) link_NAG-ASN : angle 1.62503 ( 48) link_ALPHA1-6 : bond 0.01252 ( 4) link_ALPHA1-6 : angle 2.14204 ( 12) link_BETA1-4 : bond 0.00988 ( 6) link_BETA1-4 : angle 2.73491 ( 18) link_ALPHA1-3 : bond 0.00778 ( 4) link_ALPHA1-3 : angle 1.98402 ( 12) hydrogen bonds : bond 0.03728 ( 1287) hydrogen bonds : angle 3.81355 ( 3783) metal coordination : bond 0.00148 ( 4) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.37858 ( 12) covalent geometry : bond 0.00282 (21636) covalent geometry : angle 0.58435 (29512) Misc. bond : bond 0.00059 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 2.256 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: A 323 MET cc_start: 0.7944 (mmm) cc_final: 0.7721 (mmm) REVERT: A 392 LEU cc_start: 0.9218 (mt) cc_final: 0.8825 (mt) REVERT: B 183 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8723 (t80) REVERT: C 33 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8310 (p90) REVERT: C 50 MET cc_start: 0.9012 (tpp) cc_final: 0.8467 (mpp) REVERT: C 68 ARG cc_start: 0.8414 (tpt90) cc_final: 0.8074 (tpt90) REVERT: C 198 PHE cc_start: 0.8285 (t80) cc_final: 0.8076 (t80) REVERT: C 344 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7670 (p90) REVERT: C 397 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7638 (t80) REVERT: C 407 MET cc_start: 0.8724 (tpt) cc_final: 0.8261 (tpt) REVERT: C 509 TRP cc_start: 0.7925 (m-10) cc_final: 0.7537 (m-90) REVERT: C 524 TYR cc_start: 0.8381 (t80) cc_final: 0.8103 (t80) REVERT: D 33 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8194 (p90) REVERT: D 50 MET cc_start: 0.9165 (tpp) cc_final: 0.8930 (mmp) REVERT: D 344 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7650 (p90) REVERT: D 391 TRP cc_start: 0.8343 (m100) cc_final: 0.8053 (m100) REVERT: D 397 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (t80) REVERT: D 414 ILE cc_start: 0.7810 (mt) cc_final: 0.7608 (mt) REVERT: D 509 TRP cc_start: 0.7941 (m-10) cc_final: 0.7688 (m-10) REVERT: D 524 TYR cc_start: 0.8394 (t80) cc_final: 0.8082 (t80) outliers start: 28 outliers final: 20 residues processed: 234 average time/residue: 0.2959 time to fit residues: 111.4215 Evaluate side-chains 231 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 2 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.133533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084447 restraints weight = 41060.589| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.49 r_work: 0.3049 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21678 Z= 0.154 Angle : 0.608 11.598 29614 Z= 0.289 Chirality : 0.042 0.248 3374 Planarity : 0.004 0.046 3684 Dihedral : 6.768 78.520 3506 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.59 % Allowed : 14.69 % Favored : 83.72 % 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: 1.76 (0.17), residues: 2634 helix: 1.90 (0.13), residues: 1716 sheet: -0.26 (0.48), residues: 86 loop : -0.17 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 48 HIS 0.004 0.001 HIS B 34 PHE 0.042 0.001 PHE D 262 TYR 0.031 0.001 TYR B 183 ARG 0.014 0.001 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 16) link_NAG-ASN : angle 1.63017 ( 48) link_ALPHA1-6 : bond 0.01491 ( 4) link_ALPHA1-6 : angle 1.79963 ( 12) link_BETA1-4 : bond 0.01098 ( 6) link_BETA1-4 : angle 2.79336 ( 18) link_ALPHA1-3 : bond 0.00698 ( 4) link_ALPHA1-3 : angle 1.93601 ( 12) hydrogen bonds : bond 0.03804 ( 1287) hydrogen bonds : angle 3.84788 ( 3783) metal coordination : bond 0.00176 ( 4) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.39345 ( 12) covalent geometry : bond 0.00359 (21636) covalent geometry : angle 0.59941 (29512) Misc. bond : bond 0.00081 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12089.11 seconds wall clock time: 209 minutes 11.73 seconds (12551.73 seconds total)