Starting phenix.real_space_refine on Mon Dec 11 22:32:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/12_2023/8dze_27795_updated.pdb" } resolution = 2.99 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= 0.061 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 6 6.06 5 P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3390 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D ASP 422": "OD1" <-> "OD2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ASP 341": "OD1" <-> "OD2" Residue "E ASP 422": "OD1" <-> "OD2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F ASP 341": "OD1" <-> "OD2" Residue "F ASP 422": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 403 90.435 129.403 30.842 1.00 67.86 S ATOM 2191 SG CYS A 406 94.137 129.562 30.333 1.00 74.08 S ATOM 2475 SG CYS A 445 92.459 132.497 31.856 1.00 91.66 S ATOM 2481 SG CYS A 446 92.806 129.072 33.819 1.00 87.17 S ATOM 5357 SG CYS B 403 31.594 115.078 30.834 1.00 71.28 S ATOM 5377 SG CYS B 406 33.305 118.364 30.321 1.00 77.86 S ATOM 5661 SG CYS B 445 29.924 118.377 31.845 1.00 92.91 S ATOM 5667 SG CYS B 446 33.066 116.970 33.808 1.00 87.02 S ATOM 8543 SG CYS C 403 14.588 56.945 30.844 1.00 71.62 S ATOM 8563 SG CYS C 406 12.597 60.069 30.330 1.00 77.94 S ATOM 8847 SG CYS C 445 10.896 57.148 31.855 1.00 90.02 S ATOM 8853 SG CYS C 446 13.685 59.166 33.817 1.00 86.54 S ATOM 11729 SG CYS D 403 56.450 13.154 30.852 1.00 67.81 S ATOM 11749 SG CYS D 406 52.749 12.993 30.339 1.00 74.11 S ATOM 12033 SG CYS D 445 54.428 10.060 31.864 1.00 91.67 S ATOM 12039 SG CYS D 446 54.076 13.485 33.825 1.00 87.38 S ATOM 14915 SG CYS E 403 115.291 27.493 30.852 1.00 70.69 S ATOM 14935 SG CYS E 406 113.582 24.206 30.338 1.00 76.98 S ATOM 15219 SG CYS E 445 116.961 24.194 31.864 1.00 92.46 S ATOM 15225 SG CYS E 446 113.818 25.599 33.825 1.00 86.08 S ATOM 18101 SG CYS F 403 132.266 85.643 30.857 1.00 71.42 S ATOM 18121 SG CYS F 406 134.258 82.519 30.345 1.00 78.04 S ATOM 18405 SG CYS F 445 135.958 85.440 31.871 1.00 90.30 S ATOM 18411 SG CYS F 446 133.167 83.422 33.831 1.00 86.50 S Time building chain proxies: 10.31, per 1000 atoms: 0.53 Number of scatterers: 19308 At special positions: 0 Unit cell: (147.96, 143.64, 81, 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 6 29.99 S 84 16.00 P 18 15.00 O 3708 8.00 N 3390 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.98 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 403 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 446 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 403 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 446 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 403 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 446 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 403 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 446 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 403 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 446 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 403 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 446 " Number of angles added : 36 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 18 sheets defined 38.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 266 through 281 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 521 through 532 Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 266 through 281 Processing helix chain 'C' and resid 312 through 328 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 369 through 375 Processing helix chain 'C' and resid 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 422 through 428 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 521 through 532 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 266 through 281 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 369 through 375 Processing helix chain 'D' and resid 381 through 384 No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 410 through 415 Processing helix chain 'D' and resid 422 through 428 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 521 through 532 Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 239 through 250 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 266 through 281 Processing helix chain 'E' and resid 312 through 328 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 381 through 384 No H-bonds generated for 'chain 'E' and resid 381 through 384' Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 422 through 428 Processing helix chain 'E' and resid 464 through 471 Processing helix chain 'E' and resid 479 through 484 Processing helix chain 'E' and resid 491 through 501 Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 516 through 518 No H-bonds generated for 'chain 'E' and resid 516 through 518' Processing helix chain 'E' and resid 521 through 532 Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 239 through 250 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 266 through 281 Processing helix chain 'F' and resid 312 through 328 Processing helix chain 'F' and resid 342 through 354 Processing helix chain 'F' and resid 369 through 375 Processing helix chain 'F' and resid 381 through 384 No H-bonds generated for 'chain 'F' and resid 381 through 384' Processing helix chain 'F' and resid 410 through 415 Processing helix chain 'F' and resid 422 through 428 Processing helix chain 'F' and resid 464 through 471 Processing helix chain 'F' and resid 479 through 484 Processing helix chain 'F' and resid 491 through 501 Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 521 through 532 Processing sheet with id= A, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 257 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 393 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER A 259 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 395 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 288 through 290 removed outlier: 5.599A pdb=" N ALA A 302 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE B 257 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU B 393 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER B 259 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 395 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 288 through 290 removed outlier: 5.599A pdb=" N ALA B 302 " --> pdb=" O SER B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE C 257 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU C 393 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER C 259 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 395 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 288 through 290 removed outlier: 5.599A pdb=" N ALA C 302 " --> pdb=" O SER C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE D 257 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU D 393 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER D 259 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 395 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 288 through 290 removed outlier: 5.599A pdb=" N ALA D 302 " --> pdb=" O SER D 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE E 257 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU E 393 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER E 259 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA E 395 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 288 through 290 removed outlier: 5.600A pdb=" N ALA E 302 " --> pdb=" O SER E 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 357 through 361 removed outlier: 6.523A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE F 257 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU F 393 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER F 259 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA F 395 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 288 through 290 removed outlier: 5.599A pdb=" N ALA F 302 " --> pdb=" O SER F 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 756 hydrogen bonds defined for protein. 2232 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: 5.83 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6492 1.34 - 1.46: 3958 1.46 - 1.58: 9008 1.58 - 1.70: 24 1.70 - 1.82: 144 Bond restraints: 19626 Sorted by residual: bond pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP B 602 " pdb=" C2' ANP B 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP C 602 " pdb=" C2' ANP C 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP F 602 " pdb=" C2' ANP F 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP E 602 " pdb=" C2' ANP E 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.27: 619 107.27 - 113.94: 11285 113.94 - 120.61: 7811 120.61 - 127.28: 6680 127.28 - 133.96: 209 Bond angle restraints: 26604 Sorted by residual: angle pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" O5' ANP B 602 " ideal model delta sigma weight residual 98.09 109.44 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" O5' ANP C 602 " ideal model delta sigma weight residual 98.09 109.43 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP F 602 " pdb=" PA ANP F 602 " pdb=" O5' ANP F 602 " ideal model delta sigma weight residual 98.09 109.40 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3A ANP E 602 " pdb=" PA ANP E 602 " pdb=" O5' ANP E 602 " ideal model delta sigma weight residual 98.09 109.39 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3A ANP D 602 " pdb=" PA ANP D 602 " pdb=" O5' ANP D 602 " ideal model delta sigma weight residual 98.09 109.39 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 26599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 11379 30.12 - 60.24: 645 60.24 - 90.36: 18 90.36 - 120.48: 0 120.48 - 150.60: 6 Dihedral angle restraints: 12048 sinusoidal: 4848 harmonic: 7200 Sorted by residual: dihedral pdb=" O1A ANP A 602 " pdb=" O3A ANP A 602 " pdb=" PA ANP A 602 " pdb=" PB ANP A 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A ANP C 602 " pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A ANP B 602 " pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2625 0.066 - 0.133: 423 0.133 - 0.199: 6 0.199 - 0.265: 6 0.265 - 0.331: 6 Chirality restraints: 3066 Sorted by residual: chirality pdb=" C2' ANP E 602 " pdb=" C1' ANP E 602 " pdb=" C3' ANP E 602 " pdb=" O2' ANP E 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C2' ANP F 602 " pdb=" C1' ANP F 602 " pdb=" C3' ANP F 602 " pdb=" O2' ANP F 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C2' ANP C 602 " pdb=" C1' ANP C 602 " pdb=" C3' ANP C 602 " pdb=" O2' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3063 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 120 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" CD GLU A 120 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 120 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 120 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 120 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CD GLU B 120 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 120 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 120 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 120 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CD GLU D 120 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU D 120 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 120 " -0.012 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4878 2.81 - 3.33: 17750 3.33 - 3.86: 30157 3.86 - 4.38: 35942 4.38 - 4.90: 63331 Nonbonded interactions: 152058 Sorted by model distance: nonbonded pdb=" O THR D 350 " pdb=" OG1 THR D 354 " model vdw 2.289 2.440 nonbonded pdb=" O THR E 350 " pdb=" OG1 THR E 354 " model vdw 2.289 2.440 nonbonded pdb=" O THR C 350 " pdb=" OG1 THR C 354 " model vdw 2.289 2.440 nonbonded pdb=" O THR F 350 " pdb=" OG1 THR F 354 " model vdw 2.290 2.440 nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.290 2.440 ... (remaining 152053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.790 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: 4.560 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 55.420 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.008 0.236 19626 Z= 0.481 Angle : 0.825 11.347 26604 Z= 0.370 Chirality : 0.047 0.331 3066 Planarity : 0.005 0.061 3402 Dihedral : 16.651 150.605 7380 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.04 % Favored : 92.72 % Rotamer: Outliers : 0.64 % Allowed : 17.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2430 helix: 0.74 (0.15), residues: 1032 sheet: 2.20 (0.25), residues: 426 loop : -2.23 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.001 0.000 HIS E 238 PHE 0.011 0.001 PHE C 382 TYR 0.008 0.001 TYR F 278 ARG 0.015 0.001 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 2.309 Fit side-chains outliers start: 13 outliers final: 17 residues processed: 202 average time/residue: 1.2876 time to fit residues: 295.0002 Evaluate side-chains 189 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 14 average time/residue: 0.2320 time to fit residues: 8.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 0.1980 chunk 223 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 439 ASN B 256 ASN B 439 ASN C 256 ASN C 439 ASN D 256 ASN D 439 ASN E 256 ASN E 439 ASN F 256 ASN F 439 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19626 Z= 0.155 Angle : 0.470 5.540 26604 Z= 0.241 Chirality : 0.041 0.157 3066 Planarity : 0.004 0.034 3402 Dihedral : 10.414 159.577 2874 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.86 % Favored : 91.89 % Rotamer: Outliers : 2.98 % Allowed : 15.08 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2430 helix: 1.31 (0.16), residues: 1044 sheet: 2.13 (0.24), residues: 426 loop : -2.21 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 482 HIS 0.003 0.001 HIS D 238 PHE 0.008 0.001 PHE E 382 TYR 0.008 0.001 TYR B 138 ARG 0.007 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 2.238 Fit side-chains outliers start: 60 outliers final: 28 residues processed: 227 average time/residue: 1.4559 time to fit residues: 371.2092 Evaluate side-chains 207 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 13 average time/residue: 0.3576 time to fit residues: 9.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 152 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 ASN D 166 ASN F 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.194 Angle : 0.488 7.824 26604 Z= 0.251 Chirality : 0.042 0.161 3066 Planarity : 0.004 0.038 3402 Dihedral : 9.721 153.705 2874 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.57 % Favored : 92.18 % Rotamer: Outliers : 3.87 % Allowed : 14.29 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2430 helix: 1.58 (0.16), residues: 1044 sheet: 1.97 (0.24), residues: 432 loop : -2.27 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.004 0.001 HIS D 239 PHE 0.008 0.001 PHE F 204 TYR 0.011 0.001 TYR D 138 ARG 0.010 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 208 time to evaluate : 2.042 Fit side-chains outliers start: 78 outliers final: 46 residues processed: 251 average time/residue: 1.4311 time to fit residues: 401.1448 Evaluate side-chains 232 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 26 residues processed: 24 average time/residue: 0.3710 time to fit residues: 15.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 166 ASN D 166 ASN F 166 ASN F 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19626 Z= 0.199 Angle : 0.482 5.548 26604 Z= 0.252 Chirality : 0.042 0.155 3066 Planarity : 0.004 0.047 3402 Dihedral : 9.631 154.658 2874 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Rotamer: Outliers : 3.87 % Allowed : 15.23 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2430 helix: 1.44 (0.16), residues: 1080 sheet: 2.00 (0.24), residues: 426 loop : -2.29 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 359 HIS 0.004 0.001 HIS C 239 PHE 0.007 0.001 PHE D 382 TYR 0.011 0.001 TYR A 138 ARG 0.009 0.001 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 188 time to evaluate : 2.140 Fit side-chains outliers start: 78 outliers final: 52 residues processed: 238 average time/residue: 1.2878 time to fit residues: 346.8073 Evaluate side-chains 236 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 184 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 36 residues processed: 18 average time/residue: 0.3406 time to fit residues: 11.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 0.0980 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 166 ASN C 127 HIS C 166 ASN D 127 HIS D 166 ASN E 166 ASN F 127 HIS F 166 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19626 Z= 0.240 Angle : 0.512 7.450 26604 Z= 0.266 Chirality : 0.043 0.163 3066 Planarity : 0.004 0.061 3402 Dihedral : 9.694 152.468 2874 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.61 % Favored : 92.14 % Rotamer: Outliers : 4.46 % Allowed : 15.43 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2430 helix: 1.43 (0.16), residues: 1080 sheet: 1.90 (0.24), residues: 426 loop : -2.33 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.005 0.001 HIS F 239 PHE 0.009 0.001 PHE B 218 TYR 0.010 0.001 TYR A 138 ARG 0.010 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 191 time to evaluate : 2.182 Fit side-chains outliers start: 90 outliers final: 58 residues processed: 254 average time/residue: 1.3053 time to fit residues: 373.6920 Evaluate side-chains 229 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 171 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 46 residues processed: 13 average time/residue: 0.3941 time to fit residues: 10.2503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.0570 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 166 ASN D 166 ASN E 166 ASN F 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19626 Z= 0.161 Angle : 0.472 5.508 26604 Z= 0.247 Chirality : 0.041 0.135 3066 Planarity : 0.004 0.043 3402 Dihedral : 9.573 153.283 2874 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 4.22 % Allowed : 16.02 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2430 helix: 1.56 (0.16), residues: 1080 sheet: 1.91 (0.24), residues: 426 loop : -2.31 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.002 0.001 HIS A 239 PHE 0.007 0.001 PHE E 218 TYR 0.009 0.001 TYR D 138 ARG 0.008 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 178 time to evaluate : 2.193 Fit side-chains outliers start: 85 outliers final: 57 residues processed: 235 average time/residue: 1.3392 time to fit residues: 355.5941 Evaluate side-chains 235 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 46 residues processed: 11 average time/residue: 0.4032 time to fit residues: 9.1167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 134 optimal weight: 0.0470 chunk 200 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 166 ASN E 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19626 Z= 0.170 Angle : 0.478 7.042 26604 Z= 0.248 Chirality : 0.042 0.137 3066 Planarity : 0.004 0.048 3402 Dihedral : 9.511 153.415 2874 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 4.02 % Allowed : 16.17 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2430 helix: 1.59 (0.16), residues: 1080 sheet: 1.91 (0.24), residues: 426 loop : -2.31 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.003 0.001 HIS F 239 PHE 0.007 0.001 PHE B 382 TYR 0.016 0.001 TYR A 174 ARG 0.010 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 183 time to evaluate : 2.374 Fit side-chains outliers start: 81 outliers final: 60 residues processed: 243 average time/residue: 1.4231 time to fit residues: 387.2978 Evaluate side-chains 241 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 2.185 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 46 residues processed: 14 average time/residue: 0.5475 time to fit residues: 12.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 141 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19626 Z= 0.156 Angle : 0.474 6.169 26604 Z= 0.246 Chirality : 0.041 0.134 3066 Planarity : 0.004 0.043 3402 Dihedral : 9.456 153.978 2874 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 3.27 % Allowed : 17.26 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2430 helix: 1.59 (0.16), residues: 1092 sheet: 1.92 (0.24), residues: 426 loop : -2.29 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.002 0.000 HIS C 239 PHE 0.007 0.001 PHE D 218 TYR 0.015 0.001 TYR D 174 ARG 0.009 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 177 time to evaluate : 2.276 Fit side-chains outliers start: 66 outliers final: 57 residues processed: 227 average time/residue: 1.3469 time to fit residues: 346.3456 Evaluate side-chains 227 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 47 residues processed: 10 average time/residue: 0.7408 time to fit residues: 12.1126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.0470 chunk 227 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19626 Z= 0.159 Angle : 0.480 7.168 26604 Z= 0.248 Chirality : 0.041 0.134 3066 Planarity : 0.004 0.050 3402 Dihedral : 9.410 154.135 2874 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 3.17 % Allowed : 17.36 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2430 helix: 1.66 (0.16), residues: 1092 sheet: 1.92 (0.24), residues: 426 loop : -2.29 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 359 HIS 0.003 0.001 HIS C 239 PHE 0.007 0.001 PHE E 204 TYR 0.018 0.001 TYR A 174 ARG 0.013 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 177 time to evaluate : 2.324 Fit side-chains outliers start: 64 outliers final: 55 residues processed: 228 average time/residue: 1.2585 time to fit residues: 326.0774 Evaluate side-chains 230 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 46 residues processed: 9 average time/residue: 0.5505 time to fit residues: 9.4662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 195 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19626 Z= 0.193 Angle : 0.497 6.833 26604 Z= 0.257 Chirality : 0.042 0.137 3066 Planarity : 0.004 0.060 3402 Dihedral : 9.437 152.530 2874 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.64 % Favored : 91.11 % Rotamer: Outliers : 2.83 % Allowed : 17.86 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2430 helix: 1.63 (0.16), residues: 1092 sheet: 1.03 (0.24), residues: 504 loop : -2.20 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 359 HIS 0.004 0.001 HIS C 239 PHE 0.008 0.001 PHE D 218 TYR 0.010 0.001 TYR D 138 ARG 0.013 0.000 ARG F 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 188 time to evaluate : 2.237 Fit side-chains outliers start: 57 outliers final: 50 residues processed: 240 average time/residue: 1.3648 time to fit residues: 369.1803 Evaluate side-chains 228 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 2 average time/residue: 0.7026 time to fit residues: 4.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 195 optimal weight: 0.0020 chunk 81 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112181 restraints weight = 21839.724| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.27 r_work: 0.3176 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19626 Z= 0.137 Angle : 0.477 7.433 26604 Z= 0.246 Chirality : 0.041 0.132 3066 Planarity : 0.004 0.056 3402 Dihedral : 9.352 154.392 2874 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 2.98 % Allowed : 18.01 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2430 helix: 1.73 (0.16), residues: 1092 sheet: 1.95 (0.24), residues: 426 loop : -2.27 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 359 HIS 0.002 0.000 HIS D 238 PHE 0.007 0.001 PHE E 382 TYR 0.011 0.001 TYR D 174 ARG 0.013 0.000 ARG F 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6343.18 seconds wall clock time: 114 minutes 36.26 seconds (6876.26 seconds total)