Starting phenix.real_space_refine on Sun Sep 29 02:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_17381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_17381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_17381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_17381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p30_17381/09_2024/8p30_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-5461/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: 20.16, per 1000 atoms: 0.96 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=3, 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 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: 5.64 Conformation dependent library (CDL) restraints added in 2.7 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: 1.94 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: 6.90 Time building geometry restraints manager: 6.66 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: 12345 23.80 - 47.60: 508 47.60 - 71.39: 80 71.39 - 95.19: 32 95.19 - 118.99: 16 Dihedral angle restraints: 12981 sinusoidal: 5245 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 12978 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: 161 2.60 - 3.18: 18641 3.18 - 3.75: 33729 3.75 - 4.33: 45305 4.33 - 4.90: 75541 Nonbonded interactions: 173377 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 B 530 " pdb=" SG CYS B 542 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 344 " pdb=" SG CYS B 361 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 309 " pdb=" SG CYS C 358 " model vdw 2.032 3.760 ... (remaining 173372 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: 0.00 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 57.620 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.540 ------------------------------------------------------------------------------- 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 21636 Z= 0.226 Angle : 0.588 8.682 29512 Z= 0.299 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 445 time to evaluate : 2.241 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: 0.3357 time to fit residues: 233.4196 Evaluate side-chains 242 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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: 1.9990 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 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: 1.7984 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21636 Z= 0.259 Angle : 0.607 12.768 29512 Z= 0.300 Chirality : 0.043 0.278 3374 Planarity : 0.004 0.076 3684 Dihedral : 10.308 109.377 3508 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.43 % Allowed : 11.66 % 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: 1.51 (0.17), residues: 2634 helix: 1.79 (0.13), residues: 1702 sheet: 0.21 (0.52), residues: 82 loop : -0.50 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 48 HIS 0.008 0.001 HIS A 34 PHE 0.024 0.002 PHE B 40 TYR 0.016 0.002 TYR B 516 ARG 0.005 0.001 ARG A 192 *********************** 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 301 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 249 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TRP cc_start: 0.7902 (m100) cc_final: 0.7306 (m100) REVERT: A 462 MET cc_start: 0.7920 (mtt) cc_final: 0.6981 (mtm) REVERT: B 48 TRP cc_start: 0.8861 (t-100) cc_final: 0.8619 (t60) REVERT: B 302 TRP cc_start: 0.7877 (m100) cc_final: 0.7537 (m100) REVERT: B 306 ARG cc_start: 0.8696 (ptm160) cc_final: 0.8201 (ttp80) REVERT: B 323 MET cc_start: 0.8181 (mmm) cc_final: 0.7926 (mmm) REVERT: B 376 MET cc_start: 0.9010 (ttm) cc_final: 0.8671 (ttt) REVERT: B 401 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8013 (t70) REVERT: B 462 MET cc_start: 0.7921 (mtt) cc_final: 0.6985 (mtm) REVERT: C 50 MET cc_start: 0.8761 (tpp) cc_final: 0.8373 (mmp) REVERT: C 68 ARG cc_start: 0.8615 (tpt90) cc_final: 0.8073 (tpt90) REVERT: C 69 MET cc_start: 0.8463 (mmp) cc_final: 0.8240 (mmp) REVERT: C 241 TRP cc_start: 0.7656 (m100) cc_final: 0.7391 (m-10) REVERT: C 325 ASP cc_start: 0.6903 (t0) cc_final: 0.6610 (t0) REVERT: C 385 MET cc_start: 0.7593 (mmt) cc_final: 0.7247 (mmt) REVERT: C 512 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8020 (m) REVERT: D 50 MET cc_start: 0.8742 (tpp) cc_final: 0.8370 (mmp) REVERT: D 68 ARG cc_start: 0.8574 (tpt90) cc_final: 0.8110 (tpt90) REVERT: D 69 MET cc_start: 0.8451 (mmp) cc_final: 0.8204 (mmp) REVERT: D 437 VAL cc_start: 0.9123 (t) cc_final: 0.8865 (p) REVERT: D 512 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8022 (m) REVERT: D 545 GLN cc_start: 0.7240 (mt0) cc_final: 0.6896 (mt0) outliers start: 52 outliers final: 22 residues processed: 286 average time/residue: 0.3337 time to fit residues: 148.4061 Evaluate side-chains 231 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain D residue 125 VAL 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 393 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 VAL 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 132 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 543 GLN D 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21636 Z= 0.191 Angle : 0.572 12.538 29512 Z= 0.279 Chirality : 0.042 0.276 3374 Planarity : 0.004 0.060 3684 Dihedral : 9.368 106.170 3508 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.59 % Allowed : 12.97 % Favored : 85.45 % 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: 1.65 (0.16), residues: 2634 helix: 1.87 (0.13), residues: 1716 sheet: 0.29 (0.52), residues: 82 loop : -0.42 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 509 HIS 0.008 0.001 HIS B 34 PHE 0.022 0.001 PHE B 40 TYR 0.012 0.001 TYR C 60 ARG 0.007 0.001 ARG D 70 *********************** 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 260 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 2.277 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 306 ARG cc_start: 0.8952 (ptm160) cc_final: 0.8630 (ttp80) REVERT: B 48 TRP cc_start: 0.8774 (t-100) cc_final: 0.8374 (t-100) REVERT: B 302 TRP cc_start: 0.7832 (m100) cc_final: 0.7527 (m100) REVERT: B 323 MET cc_start: 0.8288 (mmm) cc_final: 0.7900 (mmm) REVERT: B 376 MET cc_start: 0.9069 (ttm) cc_final: 0.8701 (ttt) REVERT: B 401 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (t70) REVERT: C 33 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7425 (p90) REVERT: C 68 ARG cc_start: 0.8334 (tpt90) cc_final: 0.8007 (tpt90) REVERT: C 241 TRP cc_start: 0.7574 (m100) cc_final: 0.7318 (m-10) REVERT: C 385 MET cc_start: 0.7659 (mmt) cc_final: 0.7323 (mmt) REVERT: C 397 PHE cc_start: 0.7710 (t80) cc_final: 0.7397 (t80) REVERT: C 407 MET cc_start: 0.8292 (tpt) cc_final: 0.7859 (tpt) REVERT: C 509 TRP cc_start: 0.7526 (m-10) cc_final: 0.6974 (m-90) REVERT: C 524 TYR cc_start: 0.8464 (t80) cc_final: 0.8145 (t80) REVERT: D 33 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7417 (p90) REVERT: D 50 MET cc_start: 0.8789 (tpp) cc_final: 0.8480 (mmp) REVERT: D 68 ARG cc_start: 0.8413 (tpt90) cc_final: 0.8092 (tpt90) REVERT: D 407 MET cc_start: 0.8312 (tpt) cc_final: 0.7886 (tpt) REVERT: D 437 VAL cc_start: 0.9149 (t) cc_final: 0.8927 (p) REVERT: D 509 TRP cc_start: 0.7377 (m-10) cc_final: 0.6826 (m-90) outliers start: 34 outliers final: 17 residues processed: 253 average time/residue: 0.3070 time to fit residues: 121.9019 Evaluate side-chains 226 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 C residue 475 VAL Chi-restraints excluded: chain C residue 501 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 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 235 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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** D 67 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21636 Z= 0.156 Angle : 0.540 11.871 29512 Z= 0.262 Chirality : 0.041 0.267 3374 Planarity : 0.004 0.052 3684 Dihedral : 8.396 102.799 3508 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 13.34 % Favored : 85.03 % 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: 1.73 (0.17), residues: 2634 helix: 1.92 (0.13), residues: 1734 sheet: 0.23 (0.51), residues: 86 loop : -0.39 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 302 HIS 0.005 0.001 HIS A 34 PHE 0.028 0.001 PHE B 40 TYR 0.012 0.001 TYR D 101 ARG 0.005 0.000 ARG A 306 *********************** 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 268 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 2.205 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: B 48 TRP cc_start: 0.8837 (t-100) cc_final: 0.8394 (t-100) REVERT: B 302 TRP cc_start: 0.7788 (m100) cc_final: 0.7582 (m100) REVERT: B 323 MET cc_start: 0.8205 (mmm) cc_final: 0.7942 (mmm) REVERT: B 376 MET cc_start: 0.9085 (ttm) cc_final: 0.8715 (ttt) REVERT: B 401 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7800 (t70) REVERT: C 33 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7316 (p90) REVERT: C 50 MET cc_start: 0.8708 (tpp) cc_final: 0.8146 (mpp) REVERT: C 68 ARG cc_start: 0.8525 (tpt90) cc_final: 0.8162 (tpt90) REVERT: C 198 PHE cc_start: 0.8411 (t80) cc_final: 0.8192 (t80) REVERT: C 397 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7443 (t80) REVERT: C 407 MET cc_start: 0.8341 (tpt) cc_final: 0.7909 (tpt) REVERT: C 414 ILE cc_start: 0.7757 (mt) cc_final: 0.7466 (mt) REVERT: C 509 TRP cc_start: 0.7576 (m-10) cc_final: 0.7222 (m-90) REVERT: C 524 TYR cc_start: 0.8506 (t80) cc_final: 0.8206 (t80) REVERT: D 33 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7136 (p90) REVERT: D 50 MET cc_start: 0.8841 (tpp) cc_final: 0.8577 (mmp) REVERT: D 68 ARG cc_start: 0.8542 (tpt90) cc_final: 0.8129 (tpt90) REVERT: D 407 MET cc_start: 0.8517 (tpt) cc_final: 0.8114 (tpt) REVERT: D 414 ILE cc_start: 0.7758 (mt) cc_final: 0.7471 (mt) REVERT: D 437 VAL cc_start: 0.9101 (t) cc_final: 0.8889 (p) REVERT: D 509 TRP cc_start: 0.7604 (m-10) cc_final: 0.7201 (m-90) outliers start: 35 outliers final: 17 residues processed: 260 average time/residue: 0.3161 time to fit residues: 128.9123 Evaluate side-chains 231 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 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 328 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 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 328 LEU 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 210 optimal weight: 5.9990 chunk 143 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 0.0770 chunk 216 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21636 Z= 0.191 Angle : 0.544 12.053 29512 Z= 0.264 Chirality : 0.041 0.264 3374 Planarity : 0.004 0.049 3684 Dihedral : 8.099 100.165 3508 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.54 % Allowed : 13.81 % Favored : 84.65 % 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: 1.75 (0.16), residues: 2634 helix: 1.97 (0.13), residues: 1718 sheet: 0.19 (0.50), residues: 86 loop : -0.42 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 77 HIS 0.005 0.001 HIS A 34 PHE 0.023 0.001 PHE C 96 TYR 0.011 0.001 TYR D 101 ARG 0.009 0.001 ARG C 78 *********************** 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 260 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.7976 (tmm) cc_final: 0.7652 (tmm) REVERT: A 392 LEU cc_start: 0.9249 (mt) cc_final: 0.8870 (mt) REVERT: B 48 TRP cc_start: 0.8844 (t-100) cc_final: 0.8411 (t-100) REVERT: B 323 MET cc_start: 0.8272 (mmm) cc_final: 0.8007 (mmm) REVERT: B 376 MET cc_start: 0.9116 (ttm) cc_final: 0.8854 (ttt) REVERT: C 33 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7437 (p90) REVERT: C 50 MET cc_start: 0.8779 (tpp) cc_final: 0.8130 (mpp) REVERT: C 68 ARG cc_start: 0.8497 (tpt90) cc_final: 0.8106 (tpt90) REVERT: C 198 PHE cc_start: 0.8365 (t80) cc_final: 0.8146 (t80) REVERT: C 397 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7396 (t80) REVERT: C 407 MET cc_start: 0.8463 (tpt) cc_final: 0.8067 (tpt) REVERT: C 414 ILE cc_start: 0.7807 (mt) cc_final: 0.7527 (mt) REVERT: C 509 TRP cc_start: 0.7785 (m-10) cc_final: 0.7339 (m-90) REVERT: D 33 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7428 (p90) REVERT: D 50 MET cc_start: 0.8852 (tpp) cc_final: 0.8606 (mmp) REVERT: D 68 ARG cc_start: 0.8511 (tpt90) cc_final: 0.8115 (tpt90) REVERT: D 407 MET cc_start: 0.8503 (tpt) cc_final: 0.8101 (tpt) REVERT: D 414 ILE cc_start: 0.7792 (mt) cc_final: 0.7517 (mt) REVERT: D 476 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7481 (mt-10) REVERT: D 509 TRP cc_start: 0.7735 (m-10) cc_final: 0.7383 (m-90) outliers start: 33 outliers final: 20 residues processed: 252 average time/residue: 0.3111 time to fit residues: 123.8972 Evaluate side-chains 231 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 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 328 LEU Chi-restraints excluded: chain C residue 358 CYS 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 475 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21636 Z= 0.190 Angle : 0.557 11.841 29512 Z= 0.267 Chirality : 0.041 0.258 3374 Planarity : 0.004 0.047 3684 Dihedral : 7.824 97.389 3506 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 14.74 % Favored : 83.77 % 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: 1.82 (0.16), residues: 2634 helix: 2.01 (0.13), residues: 1714 sheet: 0.10 (0.50), residues: 86 loop : -0.33 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 69 HIS 0.009 0.001 HIS B 540 PHE 0.027 0.001 PHE D 96 TYR 0.012 0.001 TYR D 101 ARG 0.015 0.001 ARG C 70 *********************** 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 247 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.258 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: 0.7906 (tmm) cc_final: 0.7594 (tmm) REVERT: A 392 LEU cc_start: 0.9255 (mt) cc_final: 0.8868 (mt) REVERT: B 48 TRP cc_start: 0.8757 (t-100) cc_final: 0.8320 (t-100) REVERT: B 323 MET cc_start: 0.8225 (mmm) cc_final: 0.7977 (mmm) REVERT: B 360 MET cc_start: 0.7797 (tmm) cc_final: 0.7566 (tmm) REVERT: B 376 MET cc_start: 0.9178 (ttm) cc_final: 0.8844 (ttt) REVERT: B 408 MET cc_start: 0.9058 (mmm) cc_final: 0.8823 (mmm) REVERT: C 33 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7659 (p90) REVERT: C 50 MET cc_start: 0.8769 (tpp) cc_final: 0.8191 (mpp) REVERT: C 68 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8036 (tpt90) REVERT: C 84 LEU cc_start: 0.8293 (mm) cc_final: 0.8035 (mp) REVERT: C 198 PHE cc_start: 0.8279 (t80) cc_final: 0.8070 (t80) REVERT: C 385 MET cc_start: 0.7764 (mmt) cc_final: 0.7561 (mmt) REVERT: C 391 TRP cc_start: 0.8244 (m100) cc_final: 0.7929 (m100) REVERT: C 397 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7443 (t80) REVERT: C 407 MET cc_start: 0.8497 (tpt) cc_final: 0.8038 (tpt) REVERT: C 414 ILE cc_start: 0.7802 (mt) cc_final: 0.7523 (mt) REVERT: C 509 TRP cc_start: 0.7886 (m-10) cc_final: 0.7431 (m-90) REVERT: D 33 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7650 (p90) REVERT: D 50 MET cc_start: 0.8871 (tpp) cc_final: 0.8653 (mmp) REVERT: D 96 PHE cc_start: 0.8943 (t80) cc_final: 0.8737 (t80) REVERT: D 391 TRP cc_start: 0.8174 (m100) cc_final: 0.7902 (m100) REVERT: D 407 MET cc_start: 0.8497 (tpt) cc_final: 0.8110 (tpt) REVERT: D 414 ILE cc_start: 0.7812 (mt) cc_final: 0.7547 (mt) REVERT: D 509 TRP cc_start: 0.7810 (m-10) cc_final: 0.7483 (m-90) outliers start: 32 outliers final: 24 residues processed: 237 average time/residue: 0.2933 time to fit residues: 112.1909 Evaluate side-chains 229 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 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 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL 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 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 328 LEU Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8209 > 50: distance: 19 - 138: 19.216 distance: 22 - 135: 5.590 distance: 113 - 114: 7.900 distance: 114 - 115: 10.737 distance: 114 - 117: 4.580 distance: 115 - 116: 24.910 distance: 115 - 121: 33.159 distance: 117 - 118: 10.723 distance: 118 - 119: 13.935 distance: 118 - 120: 9.167 distance: 121 - 122: 21.298 distance: 122 - 123: 24.269 distance: 122 - 125: 12.857 distance: 123 - 124: 31.154 distance: 123 - 127: 31.114 distance: 125 - 126: 14.495 distance: 127 - 128: 17.261 distance: 128 - 129: 8.992 distance: 128 - 131: 4.135 distance: 129 - 130: 10.797 distance: 129 - 135: 12.443 distance: 131 - 132: 11.284 distance: 132 - 133: 8.016 distance: 132 - 134: 9.761 distance: 135 - 136: 5.427 distance: 136 - 137: 14.503 distance: 136 - 139: 8.802 distance: 137 - 138: 15.150 distance: 137 - 144: 19.417 distance: 139 - 140: 13.611 distance: 140 - 141: 3.404 distance: 141 - 142: 6.721 distance: 141 - 143: 3.523 distance: 144 - 145: 10.411 distance: 145 - 146: 8.674 distance: 145 - 148: 8.875 distance: 146 - 147: 4.775 distance: 146 - 155: 8.543 distance: 148 - 149: 6.665 distance: 149 - 150: 3.460 distance: 149 - 151: 6.496 distance: 151 - 153: 6.053 distance: 152 - 154: 4.274 distance: 153 - 154: 6.065 distance: 155 - 156: 3.753 distance: 156 - 157: 5.882 distance: 156 - 159: 8.060 distance: 157 - 158: 7.346 distance: 157 - 163: 12.945 distance: 159 - 160: 3.789 distance: 160 - 161: 6.579 distance: 160 - 162: 6.932 distance: 163 - 164: 17.639 distance: 164 - 165: 21.857 distance: 165 - 166: 27.267 distance: 165 - 167: 32.228 distance: 167 - 168: 10.445 distance: 168 - 169: 31.724 distance: 168 - 171: 16.233 distance: 169 - 170: 24.212 distance: 169 - 175: 12.873 distance: 171 - 172: 18.463 distance: 171 - 173: 8.929 distance: 172 - 174: 11.798 distance: 175 - 176: 6.586 distance: 176 - 177: 18.255 distance: 176 - 179: 13.706 distance: 177 - 178: 4.962 distance: 177 - 184: 14.440 distance: 179 - 180: 15.239 distance: 180 - 181: 6.346 distance: 181 - 182: 14.042 distance: 181 - 183: 15.792 distance: 184 - 185: 18.875 distance: 184 - 190: 12.147 distance: 185 - 186: 17.806 distance: 185 - 188: 10.724 distance: 186 - 187: 7.342 distance: 186 - 191: 6.664 distance: 188 - 189: 12.079 distance: 189 - 190: 19.337