Starting phenix.real_space_refine on Tue Jul 23 02:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p31_17382/07_2024/8p31_17382_neut.cif" } resolution = 3.24 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= 0.030 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 114 5.16 5 C 13420 2.51 5 N 3356 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20752 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5980 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5980 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4221 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 20, 'TRANS': 551} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4221 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 20, 'TRANS': 551} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "B" 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: "D" 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 Time building chain proxies: 12.00, per 1000 atoms: 0.58 Number of scatterers: 20752 At special positions: 0 Unit cell: (133.376, 105.953, 174.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 114 16.00 O 3860 8.00 N 3356 7.00 C 13420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.03 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=2, symmetry=0 Links applied 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: 9.44 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 378 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 374 " 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: 134 helices and 10 sheets defined 72.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.870A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.737A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.520A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (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 218 through 250 removed outlier: 3.800A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.722A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.182A 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: 4.210A 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 305 through 318 removed outlier: 3.801A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.122A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.687A 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: 3.928A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.790A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.806A 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 484 removed outlier: 3.574A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) 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: 3.777A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.636A 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 removed outlier: 3.524A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.563A 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 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 716 removed outlier: 3.503A pdb=" N ILE A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.606A 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 21 through 53 removed outlier: 3.871A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.738A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.521A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (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 218 through 250 removed outlier: 3.800A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.724A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.181A 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: 4.211A 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 305 through 318 removed outlier: 3.802A pdb=" N LYS B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.123A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.687A 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: 3.927A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.782A 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: 3.790A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 449 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 3.807A 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 484 removed outlier: 3.575A pdb=" N GLU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) 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: 3.777A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.635A 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 removed outlier: 3.524A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 removed outlier: 3.563A 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 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.503A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.606A 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 12 through 23 Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.837A 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: 3.785A pdb=" N VAL C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.570A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.936A 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: 3.592A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.527A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.626A 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: 3.906A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.748A pdb=" N TRP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.647A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.542A 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: 3.742A pdb=" N TYR C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 4.143A 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: 3.591A 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: 3.795A pdb=" N MET C 450 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.813A 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: 3.629A pdb=" N LEU C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.740A 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: 4.611A 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 12 through 23 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.837A 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: 3.786A pdb=" N VAL D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 70 removed outlier: 3.571A pdb=" N LEU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.937A 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: 3.591A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.528A pdb=" N GLY D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.627A 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: 3.906A pdb=" N GLY D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.748A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.648A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 322 removed outlier: 3.542A 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: 3.742A pdb=" N TYR D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.142A 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: 3.592A 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: 3.796A pdb=" N MET D 450 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.811A 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: 3.629A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.613A 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 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.195A 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.196A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA8, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA9, first strand: chain 'C' and resid 535 through 540 Processing sheet with id=AB1, first strand: chain 'D' and resid 535 through 540 1283 hydrogen bonds defined for protein. 3753 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: 7.02 Time building geometry restraints manager: 10.22 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: 4839 1.33 - 1.45: 4871 1.45 - 1.57: 11406 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 21304 Sorted by residual: bond pdb=" C YCP D 703 " pdb=" O YCP D 703 " ideal model delta sigma weight residual 1.231 1.307 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 1.231 1.307 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NDG A 902 " pdb=" O5 NDG A 902 " ideal model delta sigma weight residual 1.392 1.428 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sigma weight residual 1.392 1.428 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.56: 353 104.56 - 111.93: 10372 111.93 - 119.30: 7077 119.30 - 126.68: 10848 126.68 - 134.05: 422 Bond angle restraints: 29072 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 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO D 353 " pdb=" N PRO D 353 " pdb=" CD PRO D 353 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.10e+01 angle pdb=" CA YCP D 703 " pdb=" C YCP D 703 " pdb=" O YCP D 703 " ideal model delta sigma weight residual 120.80 112.67 8.13 1.70e+00 3.46e-01 2.29e+01 angle pdb=" CA YCP C 703 " pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 120.80 112.69 8.11 1.70e+00 3.46e-01 2.27e+01 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 113.71 109.63 4.08 9.50e-01 1.11e+00 1.85e+01 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 11996 22.39 - 44.77: 582 44.77 - 67.16: 84 67.16 - 89.54: 30 89.54 - 111.93: 22 Dihedral angle restraints: 12714 sinusoidal: 4982 harmonic: 7732 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 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+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 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C3 NDG B 902 " pdb=" C4 NDG B 902 " pdb=" C5 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sinusoidal sigma weight residual 53.31 -58.62 111.93 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 12711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2673 0.053 - 0.106: 555 0.106 - 0.159: 52 0.159 - 0.213: 2 0.213 - 0.266: 8 Chirality restraints: 3290 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 -2.56 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3287 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 352 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO D 353 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 353 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 353 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 352 " -0.092 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO C 353 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO C 353 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 353 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 396 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C PHE D 396 " -0.081 2.00e-02 2.50e+03 pdb=" O PHE D 396 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE D 397 " 0.028 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 294 2.68 - 3.24: 21231 3.24 - 3.79: 33890 3.79 - 4.35: 43392 4.35 - 4.90: 71731 Nonbonded interactions: 170538 Sorted by model distance: nonbonded pdb=" OH TYR C 204 " pdb=" OG1 THR C 286 " model vdw 2.129 2.440 nonbonded pdb=" OH TYR D 204 " pdb=" OG1 THR D 286 " model vdw 2.129 2.440 nonbonded pdb=" OE2 GLU D 380 " pdb=" ND2 ASN D 384 " model vdw 2.156 2.520 nonbonded pdb=" OE2 GLU C 380 " pdb=" ND2 ASN C 384 " model vdw 2.157 2.520 nonbonded pdb=" NZ LYS B 288 " pdb=" OE1 GLU B 433 " model vdw 2.203 2.520 ... (remaining 170533 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' } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.310 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.076 21304 Z= 0.248 Angle : 0.611 9.791 29072 Z= 0.327 Chirality : 0.043 0.266 3290 Planarity : 0.005 0.134 3668 Dihedral : 14.189 111.930 7720 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.68 % Allowed : 9.65 % Favored : 89.67 % 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: 1.09 (0.17), residues: 2634 helix: 1.47 (0.13), residues: 1684 sheet: 0.12 (0.65), residues: 58 loop : -0.63 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 178 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE D 460 TYR 0.016 0.001 TYR D 348 ARG 0.003 0.001 ARG C 30 *********************** 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 396 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 382 time to evaluate : 2.486 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: A 114 LYS cc_start: 0.8849 (tppt) cc_final: 0.8572 (mtpt) REVERT: A 401 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.8216 (t-90) REVERT: A 435 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7787 (mt-10) REVERT: A 713 ASP cc_start: 0.8575 (m-30) cc_final: 0.8323 (m-30) REVERT: B 114 LYS cc_start: 0.8809 (tppt) cc_final: 0.8532 (mtpp) REVERT: B 360 MET cc_start: 0.8221 (ttm) cc_final: 0.7897 (ttm) REVERT: B 393 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8082 (mtt90) REVERT: B 401 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.8017 (t-90) REVERT: B 435 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7676 (mt-10) REVERT: B 455 MET cc_start: 0.9022 (tmm) cc_final: 0.8714 (tmm) REVERT: C 213 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7244 (tpp-160) REVERT: C 406 SER cc_start: 0.8569 (m) cc_final: 0.8097 (p) REVERT: C 478 ILE cc_start: 0.8507 (mm) cc_final: 0.8240 (pt) REVERT: C 504 TYR cc_start: 0.8152 (t80) cc_final: 0.7555 (t80) REVERT: C 505 TRP cc_start: 0.8068 (m100) cc_final: 0.6777 (m100) REVERT: C 540 ASP cc_start: 0.7755 (t0) cc_final: 0.7552 (t0) REVERT: D 173 CYS cc_start: 0.8202 (m) cc_final: 0.7775 (m) REVERT: D 213 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: D 385 MET cc_start: 0.6827 (mmt) cc_final: 0.6267 (mmt) REVERT: D 406 SER cc_start: 0.8767 (m) cc_final: 0.8239 (p) REVERT: D 504 TYR cc_start: 0.8085 (t80) cc_final: 0.7438 (t80) REVERT: D 505 TRP cc_start: 0.8163 (m100) cc_final: 0.6685 (m100) REVERT: D 540 ASP cc_start: 0.7536 (t0) cc_final: 0.7294 (t0) outliers start: 14 outliers final: 2 residues processed: 394 average time/residue: 0.3257 time to fit residues: 196.7116 Evaluate side-chains 213 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 209 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 133 optimal weight: 0.0470 chunk 106 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 175 GLN A 250 ASN A 718 ASN B 139 GLN B 175 GLN B 250 ASN B 718 ASN C 67 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 222 ASN D 243 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21304 Z= 0.184 Angle : 0.555 9.895 29072 Z= 0.279 Chirality : 0.041 0.259 3290 Planarity : 0.004 0.077 3668 Dihedral : 8.230 76.525 3352 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.74 % Allowed : 13.37 % Favored : 84.89 % 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: 1.68 (0.17), residues: 2634 helix: 1.92 (0.13), residues: 1700 sheet: 0.74 (0.69), residues: 54 loop : -0.45 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 742 HIS 0.004 0.001 HIS B 34 PHE 0.024 0.001 PHE C 523 TYR 0.016 0.001 TYR B 516 ARG 0.004 0.000 ARG C 78 *********************** 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 262 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 2.332 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 50 TYR cc_start: 0.8579 (t80) cc_final: 0.8181 (t80) REVERT: A 114 LYS cc_start: 0.8816 (tppt) cc_final: 0.8536 (mtpt) REVERT: A 401 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: A 408 MET cc_start: 0.9412 (mmt) cc_final: 0.9059 (mmm) REVERT: A 480 MET cc_start: 0.8403 (mtp) cc_final: 0.8112 (mtp) REVERT: A 582 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8231 (mmm-85) REVERT: A 675 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 114 LYS cc_start: 0.8792 (tppt) cc_final: 0.8525 (mtpp) REVERT: B 190 MET cc_start: 0.8716 (tmm) cc_final: 0.8462 (tmm) REVERT: B 360 MET cc_start: 0.8151 (ttm) cc_final: 0.7951 (ttm) REVERT: B 366 MET cc_start: 0.8511 (ttm) cc_final: 0.8018 (mtp) REVERT: B 393 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8014 (mtt90) REVERT: B 408 MET cc_start: 0.9432 (mmt) cc_final: 0.9175 (mmm) REVERT: B 455 MET cc_start: 0.8981 (tmm) cc_final: 0.8617 (tmm) REVERT: B 675 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8854 (tt) REVERT: C 68 ARG cc_start: 0.7262 (tmt-80) cc_final: 0.6019 (tpp-160) REVERT: C 69 MET cc_start: 0.8316 (mmp) cc_final: 0.7891 (tpp) REVERT: C 227 MET cc_start: 0.6299 (ttt) cc_final: 0.6047 (ttt) REVERT: C 243 ASN cc_start: 0.8448 (m110) cc_final: 0.8244 (m-40) REVERT: C 406 SER cc_start: 0.8559 (m) cc_final: 0.8170 (p) REVERT: C 458 ASP cc_start: 0.9114 (m-30) cc_final: 0.8697 (m-30) REVERT: C 462 ASP cc_start: 0.8422 (t0) cc_final: 0.8112 (t0) REVERT: C 504 TYR cc_start: 0.8056 (t80) cc_final: 0.7379 (t80) REVERT: C 505 TRP cc_start: 0.8056 (m100) cc_final: 0.7041 (m100) REVERT: C 540 ASP cc_start: 0.7921 (t0) cc_final: 0.7707 (t0) REVERT: D 68 ARG cc_start: 0.7502 (tmt-80) cc_final: 0.6083 (tpp-160) REVERT: D 69 MET cc_start: 0.8224 (mmp) cc_final: 0.7486 (tpp) REVERT: D 173 CYS cc_start: 0.8174 (m) cc_final: 0.7673 (m) REVERT: D 243 ASN cc_start: 0.9041 (m110) cc_final: 0.8605 (m110) REVERT: D 406 SER cc_start: 0.8700 (m) cc_final: 0.8328 (p) REVERT: D 458 ASP cc_start: 0.9117 (m-30) cc_final: 0.8699 (m-30) REVERT: D 462 ASP cc_start: 0.8457 (t0) cc_final: 0.8140 (t0) REVERT: D 504 TYR cc_start: 0.8224 (t80) cc_final: 0.7453 (t80) REVERT: D 505 TRP cc_start: 0.8158 (m100) cc_final: 0.6861 (m100) REVERT: D 535 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8136 (mmmt) REVERT: D 540 ASP cc_start: 0.7724 (t0) cc_final: 0.7476 (t0) outliers start: 36 outliers final: 17 residues processed: 257 average time/residue: 0.3036 time to fit residues: 123.6919 Evaluate side-chains 207 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 0.0670 chunk 162 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 236 optimal weight: 0.0980 chunk 81 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 64 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 535 HIS A 718 ASN B 24 GLN B 277 ASN B 535 HIS B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 410 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21304 Z= 0.238 Angle : 0.542 8.682 29072 Z= 0.271 Chirality : 0.042 0.251 3290 Planarity : 0.004 0.059 3668 Dihedral : 6.689 76.702 3350 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 13.42 % Favored : 84.12 % 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: 1.69 (0.17), residues: 2634 helix: 1.94 (0.13), residues: 1716 sheet: 0.63 (0.64), residues: 58 loop : -0.51 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 302 HIS 0.004 0.001 HIS B 378 PHE 0.023 0.001 PHE A 28 TYR 0.022 0.001 TYR D 101 ARG 0.004 0.000 ARG A 559 *********************** 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 256 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8847 (tppt) cc_final: 0.8551 (mtpt) REVERT: A 190 MET cc_start: 0.8767 (tmm) cc_final: 0.8366 (tmm) REVERT: A 401 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8140 (t-90) REVERT: A 408 MET cc_start: 0.9370 (mmt) cc_final: 0.8969 (mmm) REVERT: A 480 MET cc_start: 0.8433 (mtp) cc_final: 0.8108 (mtp) REVERT: A 675 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9055 (tt) REVERT: B 40 PHE cc_start: 0.9305 (t80) cc_final: 0.8964 (t80) REVERT: B 114 LYS cc_start: 0.8848 (tppt) cc_final: 0.8622 (mtpt) REVERT: B 190 MET cc_start: 0.8747 (tmm) cc_final: 0.8419 (tmm) REVERT: B 366 MET cc_start: 0.8641 (ttm) cc_final: 0.8045 (mtp) REVERT: B 393 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8200 (mtt90) REVERT: B 408 MET cc_start: 0.9374 (mmt) cc_final: 0.9011 (mmm) REVERT: B 455 MET cc_start: 0.8978 (tmm) cc_final: 0.8575 (tmm) REVERT: B 675 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9043 (tt) REVERT: C 68 ARG cc_start: 0.7493 (tmt-80) cc_final: 0.6327 (tpp-160) REVERT: C 100 MET cc_start: 0.8659 (mtt) cc_final: 0.8409 (mtt) REVERT: C 225 MET cc_start: 0.7755 (ptt) cc_final: 0.7497 (ptp) REVERT: C 243 ASN cc_start: 0.8472 (m110) cc_final: 0.8159 (m-40) REVERT: C 406 SER cc_start: 0.8560 (m) cc_final: 0.8308 (p) REVERT: C 458 ASP cc_start: 0.9187 (m-30) cc_final: 0.8747 (m-30) REVERT: C 462 ASP cc_start: 0.8446 (t0) cc_final: 0.8021 (t0) REVERT: C 504 TYR cc_start: 0.8014 (t80) cc_final: 0.7813 (t80) REVERT: C 540 ASP cc_start: 0.7739 (t0) cc_final: 0.7518 (t0) REVERT: D 68 ARG cc_start: 0.7589 (tmt-80) cc_final: 0.6983 (tpp-160) REVERT: D 100 MET cc_start: 0.8645 (mtt) cc_final: 0.8399 (mtt) REVERT: D 101 TYR cc_start: 0.8079 (p90) cc_final: 0.7803 (p90) REVERT: D 173 CYS cc_start: 0.8234 (m) cc_final: 0.7730 (m) REVERT: D 227 MET cc_start: 0.6266 (ttt) cc_final: 0.6062 (ttt) REVERT: D 243 ASN cc_start: 0.9001 (m110) cc_final: 0.8570 (m110) REVERT: D 406 SER cc_start: 0.8766 (m) cc_final: 0.8452 (p) REVERT: D 458 ASP cc_start: 0.9165 (m-30) cc_final: 0.8688 (m-30) REVERT: D 462 ASP cc_start: 0.8545 (t0) cc_final: 0.8112 (t0) REVERT: D 535 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8170 (mmmt) REVERT: D 540 ASP cc_start: 0.7735 (t0) cc_final: 0.7514 (t0) outliers start: 51 outliers final: 23 residues processed: 249 average time/residue: 0.3060 time to fit residues: 120.7610 Evaluate side-chains 212 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21304 Z= 0.178 Angle : 0.517 7.735 29072 Z= 0.256 Chirality : 0.041 0.287 3290 Planarity : 0.003 0.053 3668 Dihedral : 6.135 76.361 3350 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.27 % Allowed : 13.66 % Favored : 84.07 % 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: 1.80 (0.17), residues: 2634 helix: 1.96 (0.12), residues: 1726 sheet: 0.64 (0.63), residues: 58 loop : -0.33 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 165 HIS 0.004 0.001 HIS B 378 PHE 0.012 0.001 PHE A 28 TYR 0.015 0.001 TYR B 50 ARG 0.004 0.000 ARG A 393 *********************** 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 242 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 195 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8861 (tppt) cc_final: 0.8566 (mtpt) REVERT: A 123 MET cc_start: 0.8448 (mtm) cc_final: 0.8243 (mtm) REVERT: A 190 MET cc_start: 0.8782 (tmm) cc_final: 0.8414 (tmm) REVERT: A 401 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.8057 (t-90) REVERT: A 408 MET cc_start: 0.9367 (mmt) cc_final: 0.8930 (mmm) REVERT: A 480 MET cc_start: 0.8395 (mtp) cc_final: 0.8101 (mtp) REVERT: A 675 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 40 PHE cc_start: 0.9324 (t80) cc_final: 0.8912 (t80) REVERT: B 62 MET cc_start: 0.8925 (mtm) cc_final: 0.8656 (mtm) REVERT: B 114 LYS cc_start: 0.8833 (tppt) cc_final: 0.8622 (mtpt) REVERT: B 366 MET cc_start: 0.8547 (ttm) cc_final: 0.8094 (ttm) REVERT: B 376 MET cc_start: 0.8957 (ttt) cc_final: 0.8670 (ttt) REVERT: B 408 MET cc_start: 0.9374 (mmt) cc_final: 0.8977 (mmm) REVERT: B 430 GLU cc_start: 0.8730 (pm20) cc_final: 0.8440 (mp0) REVERT: B 455 MET cc_start: 0.8968 (tmm) cc_final: 0.8552 (tmm) REVERT: B 640 MET cc_start: 0.9064 (tpt) cc_final: 0.8852 (tpp) REVERT: B 675 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9036 (tt) REVERT: C 68 ARG cc_start: 0.7582 (tmt-80) cc_final: 0.6219 (tpp-160) REVERT: C 69 MET cc_start: 0.8512 (mmt) cc_final: 0.7778 (tpp) REVERT: C 100 MET cc_start: 0.8672 (mtt) cc_final: 0.8319 (mtt) REVERT: C 243 ASN cc_start: 0.8415 (m110) cc_final: 0.8089 (m-40) REVERT: C 406 SER cc_start: 0.8731 (m) cc_final: 0.8349 (p) REVERT: C 458 ASP cc_start: 0.9208 (m-30) cc_final: 0.8767 (m-30) REVERT: C 462 ASP cc_start: 0.8384 (t0) cc_final: 0.7929 (t0) REVERT: C 540 ASP cc_start: 0.7735 (t0) cc_final: 0.7505 (t0) REVERT: D 50 MET cc_start: 0.9192 (mmp) cc_final: 0.8791 (mpp) REVERT: D 68 ARG cc_start: 0.7591 (tmt-80) cc_final: 0.7037 (tpp-160) REVERT: D 100 MET cc_start: 0.8612 (mtt) cc_final: 0.8291 (mtt) REVERT: D 173 CYS cc_start: 0.8208 (m) cc_final: 0.7684 (m) REVERT: D 225 MET cc_start: 0.7682 (ptt) cc_final: 0.7473 (ptp) REVERT: D 243 ASN cc_start: 0.8997 (m110) cc_final: 0.8773 (m-40) REVERT: D 406 SER cc_start: 0.8773 (m) cc_final: 0.8465 (p) REVERT: D 458 ASP cc_start: 0.9209 (m-30) cc_final: 0.8732 (m-30) REVERT: D 462 ASP cc_start: 0.8501 (t0) cc_final: 0.8085 (t0) REVERT: D 535 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8180 (mmmt) REVERT: D 540 ASP cc_start: 0.7758 (t0) cc_final: 0.7538 (t0) outliers start: 47 outliers final: 29 residues processed: 235 average time/residue: 0.3017 time to fit residues: 113.0422 Evaluate side-chains 215 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 216 optimal weight: 0.3980 chunk 175 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN C 106 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21304 Z= 0.172 Angle : 0.505 8.013 29072 Z= 0.250 Chirality : 0.040 0.241 3290 Planarity : 0.003 0.050 3668 Dihedral : 5.954 76.397 3350 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.27 % Allowed : 13.56 % Favored : 84.17 % 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: 1.86 (0.17), residues: 2634 helix: 2.01 (0.12), residues: 1728 sheet: 0.61 (0.63), residues: 58 loop : -0.32 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 503 HIS 0.003 0.001 HIS B 374 PHE 0.024 0.001 PHE A 40 TYR 0.013 0.001 TYR B 50 ARG 0.005 0.000 ARG B 393 *********************** 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 240 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8867 (tppt) cc_final: 0.8573 (mtpt) REVERT: A 123 MET cc_start: 0.8482 (mtm) cc_final: 0.8260 (mtm) REVERT: A 190 MET cc_start: 0.8791 (tmm) cc_final: 0.8426 (tmm) REVERT: A 401 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: A 408 MET cc_start: 0.9366 (mmt) cc_final: 0.8919 (mmm) REVERT: A 455 MET cc_start: 0.8927 (tmm) cc_final: 0.8516 (tmm) REVERT: A 480 MET cc_start: 0.8397 (mtp) cc_final: 0.8124 (mtp) REVERT: A 675 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9028 (tt) REVERT: B 40 PHE cc_start: 0.9314 (t80) cc_final: 0.8920 (t80) REVERT: B 114 LYS cc_start: 0.8841 (tppt) cc_final: 0.8636 (mtpt) REVERT: B 366 MET cc_start: 0.8530 (ttm) cc_final: 0.8111 (ttm) REVERT: B 408 MET cc_start: 0.9376 (mmt) cc_final: 0.8988 (mmm) REVERT: B 430 GLU cc_start: 0.8642 (pm20) cc_final: 0.8429 (mp0) REVERT: B 455 MET cc_start: 0.8965 (tmm) cc_final: 0.8531 (tmm) REVERT: B 640 MET cc_start: 0.9068 (tpt) cc_final: 0.8853 (tpp) REVERT: B 675 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9023 (tt) REVERT: C 68 ARG cc_start: 0.7589 (tmt-80) cc_final: 0.6239 (tpp-160) REVERT: C 69 MET cc_start: 0.8373 (mmt) cc_final: 0.7691 (tpp) REVERT: C 100 MET cc_start: 0.8657 (mtt) cc_final: 0.8291 (mtt) REVERT: C 243 ASN cc_start: 0.8456 (m110) cc_final: 0.8140 (m-40) REVERT: C 406 SER cc_start: 0.8726 (m) cc_final: 0.8359 (p) REVERT: C 458 ASP cc_start: 0.9255 (m-30) cc_final: 0.8789 (m-30) REVERT: C 462 ASP cc_start: 0.8385 (t0) cc_final: 0.7910 (t0) REVERT: C 505 TRP cc_start: 0.7913 (m100) cc_final: 0.7446 (m100) REVERT: D 50 MET cc_start: 0.9183 (mmp) cc_final: 0.8792 (mpp) REVERT: D 68 ARG cc_start: 0.7536 (tmt-80) cc_final: 0.6337 (tpp-160) REVERT: D 69 MET cc_start: 0.8446 (mmt) cc_final: 0.7490 (tpp) REVERT: D 100 MET cc_start: 0.8538 (mtt) cc_final: 0.8193 (mtt) REVERT: D 173 CYS cc_start: 0.8218 (m) cc_final: 0.7726 (m) REVERT: D 215 LEU cc_start: 0.8726 (mt) cc_final: 0.8525 (mt) REVERT: D 225 MET cc_start: 0.7808 (ptt) cc_final: 0.7344 (mtm) REVERT: D 243 ASN cc_start: 0.8996 (m110) cc_final: 0.8594 (m-40) REVERT: D 344 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6139 (p90) REVERT: D 406 SER cc_start: 0.8770 (m) cc_final: 0.8474 (p) REVERT: D 458 ASP cc_start: 0.9208 (m-30) cc_final: 0.8749 (m-30) REVERT: D 462 ASP cc_start: 0.8501 (t0) cc_final: 0.8068 (t0) REVERT: D 535 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8188 (mmmt) outliers start: 47 outliers final: 34 residues processed: 232 average time/residue: 0.2905 time to fit residues: 108.3533 Evaluate side-chains 219 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 718 ASN Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4955 > 50: distance: 6 - 28: 10.536 distance: 10 - 39: 16.321 distance: 13 - 21: 8.984 distance: 21 - 22: 4.706 distance: 22 - 23: 6.030 distance: 22 - 25: 13.980 distance: 23 - 24: 8.559 distance: 25 - 26: 21.152 distance: 25 - 27: 14.690 distance: 28 - 29: 9.134 distance: 29 - 30: 8.244 distance: 29 - 32: 8.782 distance: 30 - 31: 8.974 distance: 30 - 39: 5.897 distance: 31 - 65: 10.845 distance: 32 - 33: 15.091 distance: 33 - 34: 18.638 distance: 33 - 35: 11.055 distance: 34 - 36: 11.222 distance: 35 - 37: 19.439 distance: 36 - 38: 15.572 distance: 37 - 38: 22.500 distance: 39 - 40: 12.496 distance: 40 - 41: 20.480 distance: 40 - 43: 9.257 distance: 41 - 42: 13.481 distance: 41 - 48: 10.285 distance: 43 - 44: 36.713 distance: 44 - 45: 23.563 distance: 45 - 46: 22.536 distance: 45 - 47: 21.180 distance: 48 - 49: 9.479 distance: 49 - 50: 15.339 distance: 49 - 52: 24.537 distance: 50 - 51: 8.171 distance: 50 - 57: 10.282 distance: 52 - 53: 11.776 distance: 53 - 54: 21.319 distance: 54 - 55: 20.123 distance: 54 - 56: 8.489 distance: 57 - 58: 12.662 distance: 58 - 59: 19.555 distance: 58 - 61: 4.542 distance: 59 - 60: 13.010 distance: 59 - 65: 13.286 distance: 61 - 62: 18.104 distance: 61 - 63: 9.000 distance: 62 - 64: 14.181 distance: 65 - 66: 12.174 distance: 66 - 67: 14.402 distance: 66 - 69: 6.869 distance: 67 - 68: 21.891 distance: 67 - 74: 17.119 distance: 68 - 101: 11.345 distance: 69 - 70: 23.516 distance: 70 - 71: 21.198 distance: 71 - 72: 20.022 distance: 72 - 73: 8.247 distance: 74 - 75: 17.205 distance: 74 - 80: 20.202 distance: 75 - 76: 3.623 distance: 75 - 78: 12.951 distance: 76 - 77: 7.910 distance: 76 - 81: 12.111 distance: 79 - 80: 10.656 distance: 81 - 82: 5.028 distance: 82 - 83: 11.509 distance: 83 - 84: 13.478 distance: 83 - 89: 6.587 distance: 84 - 118: 23.755 distance: 85 - 86: 12.840 distance: 86 - 87: 18.736 distance: 86 - 88: 12.303 distance: 91 - 92: 21.317 distance: 91 - 101: 10.305 distance: 92 - 124: 12.247 distance: 93 - 94: 3.362 distance: 94 - 95: 7.034 distance: 94 - 96: 5.749 distance: 95 - 97: 13.450 distance: 96 - 98: 4.227 distance: 97 - 99: 4.586 distance: 98 - 99: 7.977 distance: 99 - 100: 15.293 distance: 101 - 102: 3.814 distance: 102 - 103: 8.401 distance: 102 - 105: 12.738 distance: 103 - 104: 6.762 distance: 103 - 110: 11.335 distance: 104 - 132: 9.162 distance: 105 - 106: 11.714 distance: 106 - 107: 6.681 distance: 107 - 108: 9.905 distance: 107 - 109: 15.451