Starting phenix.real_space_refine on Fri Mar 22 04:20:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghd_40041/03_2024/8ghd_40041_updated.pdb" } resolution = 2.2 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= 0.032 sd= 2.275 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 Fe 6 7.16 5 S 216 5.16 5 C 20616 2.51 5 N 5580 2.21 5 O 5802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "B" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "C" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "D" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "E" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "F" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 16.08, per 1000 atoms: 0.50 Number of scatterers: 32220 At special positions: 0 Unit cell: (153.34, 149.24, 104.14, 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) Fe 6 26.01 S 216 16.00 O 5802 8.00 N 5580 7.00 C 20616 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: 12.22 Conformation dependent library (CDL) restraints added in 5.2 seconds 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 24 sheets defined 44.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.70 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 168 through 194 removed outlier: 4.506A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.068A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 337 through 357 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 384 through 393 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.967A pdb=" N ALA A 417 " --> pdb=" O PHE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 459 through 482 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'A' and resid 618 through 644 removed outlier: 4.140A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 168 through 194 removed outlier: 4.528A pdb=" N LEU B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.064A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 337 through 357 Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 384 through 393 Proline residue: B 391 - end of helix Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.965A pdb=" N ALA B 417 " --> pdb=" O PHE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 459 through 482 Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 574 through 580 Processing helix chain 'B' and resid 584 through 598 Processing helix chain 'B' and resid 618 through 644 removed outlier: 4.139A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 168 through 194 removed outlier: 4.537A pdb=" N LEU C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 225 through 234 removed outlier: 4.070A pdb=" N PHE C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 337 through 357 Processing helix chain 'C' and resid 365 through 378 Processing helix chain 'C' and resid 384 through 393 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.965A pdb=" N ALA C 417 " --> pdb=" O PHE C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 459 through 482 Processing helix chain 'C' and resid 486 through 490 Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 538 through 544 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 574 through 580 Processing helix chain 'C' and resid 584 through 598 Processing helix chain 'C' and resid 618 through 644 removed outlier: 4.142A pdb=" N GLN C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 168 through 194 removed outlier: 4.517A pdb=" N LEU D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 225 through 234 removed outlier: 4.066A pdb=" N PHE D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 337 through 357 Processing helix chain 'D' and resid 365 through 378 Processing helix chain 'D' and resid 384 through 393 Proline residue: D 391 - end of helix Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.960A pdb=" N ALA D 417 " --> pdb=" O PHE D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 459 through 482 Processing helix chain 'D' and resid 486 through 490 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 538 through 544 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 584 through 598 Processing helix chain 'D' and resid 618 through 644 removed outlier: 4.141A pdb=" N GLN D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 168 through 194 removed outlier: 4.512A pdb=" N LEU E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 225 through 234 removed outlier: 4.073A pdb=" N PHE E 232 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 270 Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 337 through 357 Processing helix chain 'E' and resid 365 through 378 Processing helix chain 'E' and resid 384 through 393 Proline residue: E 391 - end of helix Processing helix chain 'E' and resid 396 through 406 Processing helix chain 'E' and resid 413 through 417 removed outlier: 3.964A pdb=" N ALA E 417 " --> pdb=" O PHE E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 439 through 441 No H-bonds generated for 'chain 'E' and resid 439 through 441' Processing helix chain 'E' and resid 443 through 449 Processing helix chain 'E' and resid 459 through 482 Processing helix chain 'E' and resid 486 through 490 Processing helix chain 'E' and resid 493 through 503 Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 538 through 544 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 554 through 556 No H-bonds generated for 'chain 'E' and resid 554 through 556' Processing helix chain 'E' and resid 574 through 580 Processing helix chain 'E' and resid 584 through 598 Processing helix chain 'E' and resid 618 through 644 removed outlier: 4.142A pdb=" N GLN E 644 " --> pdb=" O ALA E 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 168 through 194 removed outlier: 4.506A pdb=" N LEU F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 225 through 234 removed outlier: 4.076A pdb=" N PHE F 232 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 233 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 270 Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 337 through 357 Processing helix chain 'F' and resid 365 through 378 Processing helix chain 'F' and resid 384 through 393 Proline residue: F 391 - end of helix Processing helix chain 'F' and resid 396 through 406 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.960A pdb=" N ALA F 417 " --> pdb=" O PHE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 439 through 441 No H-bonds generated for 'chain 'F' and resid 439 through 441' Processing helix chain 'F' and resid 443 through 449 Processing helix chain 'F' and resid 459 through 482 Processing helix chain 'F' and resid 486 through 490 Processing helix chain 'F' and resid 493 through 503 Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 538 through 544 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 574 through 580 Processing helix chain 'F' and resid 584 through 598 Processing helix chain 'F' and resid 618 through 644 removed outlier: 4.139A pdb=" N GLN F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= C, first strand: chain 'A' and resid 32 through 38 removed outlier: 4.050A pdb=" N ARG A 21 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 273 through 277 removed outlier: 3.530A pdb=" N VAL A 315 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS A 304 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 47 through 52 Processing sheet with id= F, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= G, first strand: chain 'B' and resid 32 through 38 removed outlier: 4.059A pdb=" N ARG B 21 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.538A pdb=" N VAL B 315 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS B 304 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 47 through 52 Processing sheet with id= J, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= K, first strand: chain 'C' and resid 32 through 38 removed outlier: 4.059A pdb=" N ARG C 21 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.536A pdb=" N VAL C 315 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS C 304 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 47 through 52 Processing sheet with id= N, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= O, first strand: chain 'D' and resid 32 through 38 removed outlier: 4.058A pdb=" N ARG D 21 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 273 through 277 removed outlier: 3.535A pdb=" N VAL D 315 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS D 304 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 47 through 52 Processing sheet with id= R, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= S, first strand: chain 'E' and resid 32 through 38 removed outlier: 4.043A pdb=" N ARG E 21 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 273 through 277 removed outlier: 3.538A pdb=" N VAL E 315 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS E 304 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 47 through 52 Processing sheet with id= V, first strand: chain 'F' and resid 12 through 14 Processing sheet with id= W, first strand: chain 'F' and resid 32 through 38 removed outlier: 4.049A pdb=" N ARG F 21 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 273 through 277 removed outlier: 3.539A pdb=" N VAL F 315 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS F 304 " --> pdb=" O PRO F 313 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3906 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: 11.25 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10425 1.34 - 1.46: 5997 1.46 - 1.58: 16320 1.58 - 1.69: 6 1.69 - 1.81: 324 Bond restraints: 33072 Sorted by residual: bond pdb=" C14 ZR5 B 902 " pdb=" S1 ZR5 B 902 " ideal model delta sigma weight residual 1.539 1.751 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C14 ZR5 D 902 " pdb=" S1 ZR5 D 902 " ideal model delta sigma weight residual 1.539 1.751 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C14 ZR5 C 902 " pdb=" S1 ZR5 C 902 " ideal model delta sigma weight residual 1.539 1.751 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C14 ZR5 F 902 " pdb=" S1 ZR5 F 902 " ideal model delta sigma weight residual 1.539 1.751 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C14 ZR5 E 902 " pdb=" S1 ZR5 E 902 " ideal model delta sigma weight residual 1.539 1.750 -0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 33067 not shown) Histogram of bond angle deviations from ideal: 88.20 - 97.56: 6 97.56 - 106.93: 1388 106.93 - 116.29: 20513 116.29 - 125.66: 22116 125.66 - 135.02: 899 Bond angle restraints: 44922 Sorted by residual: angle pdb=" N ZR5 F 902 " pdb=" C8 ZR5 F 902 " pdb=" C13 ZR5 F 902 " ideal model delta sigma weight residual 92.28 120.31 -28.03 3.00e+00 1.11e-01 8.73e+01 angle pdb=" N ZR5 D 902 " pdb=" C8 ZR5 D 902 " pdb=" C13 ZR5 D 902 " ideal model delta sigma weight residual 92.28 120.25 -27.97 3.00e+00 1.11e-01 8.69e+01 angle pdb=" N ZR5 B 902 " pdb=" C8 ZR5 B 902 " pdb=" C13 ZR5 B 902 " ideal model delta sigma weight residual 92.28 120.25 -27.97 3.00e+00 1.11e-01 8.69e+01 angle pdb=" N ZR5 C 902 " pdb=" C8 ZR5 C 902 " pdb=" C13 ZR5 C 902 " ideal model delta sigma weight residual 92.28 120.23 -27.95 3.00e+00 1.11e-01 8.68e+01 angle pdb=" N ZR5 E 902 " pdb=" C8 ZR5 E 902 " pdb=" C13 ZR5 E 902 " ideal model delta sigma weight residual 92.28 120.23 -27.95 3.00e+00 1.11e-01 8.68e+01 ... (remaining 44917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 18589 21.25 - 42.50: 887 42.50 - 63.75: 240 63.75 - 85.00: 60 85.00 - 106.25: 12 Dihedral angle restraints: 19788 sinusoidal: 8244 harmonic: 11544 Sorted by residual: dihedral pdb=" C ILE D 390 " pdb=" N ILE D 390 " pdb=" CA ILE D 390 " pdb=" CB ILE D 390 " ideal model delta harmonic sigma weight residual -122.00 -131.59 9.59 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C ILE F 390 " pdb=" N ILE F 390 " pdb=" CA ILE F 390 " pdb=" CB ILE F 390 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C ILE C 390 " pdb=" N ILE C 390 " pdb=" CA ILE C 390 " pdb=" CB ILE C 390 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 19785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3993 0.063 - 0.125: 701 0.125 - 0.188: 70 0.188 - 0.250: 18 0.250 - 0.313: 12 Chirality restraints: 4794 Sorted by residual: chirality pdb=" CB ILE E 390 " pdb=" CA ILE E 390 " pdb=" CG1 ILE E 390 " pdb=" CG2 ILE E 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE C 390 " pdb=" CA ILE C 390 " pdb=" CG1 ILE C 390 " pdb=" CG2 ILE C 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE B 390 " pdb=" CA ILE B 390 " pdb=" CG1 ILE B 390 " pdb=" CG2 ILE B 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4791 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N ZR5 B 902 " -0.127 2.00e-02 2.50e+03 8.63e-02 1.49e+02 pdb=" C10 ZR5 B 902 " 0.078 2.00e-02 2.50e+03 pdb=" C11 ZR5 B 902 " 0.060 2.00e-02 2.50e+03 pdb=" C12 ZR5 B 902 " 0.076 2.00e-02 2.50e+03 pdb=" C13 ZR5 B 902 " 0.039 2.00e-02 2.50e+03 pdb=" C8 ZR5 B 902 " -0.005 2.00e-02 2.50e+03 pdb=" C9 ZR5 B 902 " 0.037 2.00e-02 2.50e+03 pdb=" S ZR5 B 902 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N ZR5 C 902 " -0.128 2.00e-02 2.50e+03 8.63e-02 1.49e+02 pdb=" C10 ZR5 C 902 " 0.078 2.00e-02 2.50e+03 pdb=" C11 ZR5 C 902 " 0.059 2.00e-02 2.50e+03 pdb=" C12 ZR5 C 902 " 0.075 2.00e-02 2.50e+03 pdb=" C13 ZR5 C 902 " 0.041 2.00e-02 2.50e+03 pdb=" C8 ZR5 C 902 " -0.004 2.00e-02 2.50e+03 pdb=" C9 ZR5 C 902 " 0.038 2.00e-02 2.50e+03 pdb=" S ZR5 C 902 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N ZR5 F 902 " -0.126 2.00e-02 2.50e+03 8.57e-02 1.47e+02 pdb=" C10 ZR5 F 902 " 0.077 2.00e-02 2.50e+03 pdb=" C11 ZR5 F 902 " 0.059 2.00e-02 2.50e+03 pdb=" C12 ZR5 F 902 " 0.075 2.00e-02 2.50e+03 pdb=" C13 ZR5 F 902 " 0.040 2.00e-02 2.50e+03 pdb=" C8 ZR5 F 902 " -0.005 2.00e-02 2.50e+03 pdb=" C9 ZR5 F 902 " 0.037 2.00e-02 2.50e+03 pdb=" S ZR5 F 902 " -0.157 2.00e-02 2.50e+03 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1562 2.73 - 3.27: 31883 3.27 - 3.82: 60951 3.82 - 4.36: 74908 4.36 - 4.90: 121583 Nonbonded interactions: 290887 Sorted by model distance: nonbonded pdb=" NE2 HIS D 365 " pdb="FE FE2 D 901 " model vdw 2.189 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.191 3.080 nonbonded pdb=" NE2 HIS F 365 " pdb="FE FE2 F 901 " model vdw 2.191 3.080 nonbonded pdb=" NE2 HIS C 365 " pdb="FE FE2 C 901 " model vdw 2.199 3.080 nonbonded pdb=" OXT ILE A 663 " pdb="FE FE2 A 901 " model vdw 2.199 3.000 ... (remaining 290882 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: 1.860 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: 0.030 Extract box with map and model: 8.670 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 82.110 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.200 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.007 0.212 33072 Z= 0.482 Angle : 1.068 28.033 44922 Z= 0.498 Chirality : 0.051 0.313 4794 Planarity : 0.010 0.129 5844 Dihedral : 14.423 106.251 12312 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 0.43 (0.12), residues: 3960 helix: 0.68 (0.11), residues: 1770 sheet: -0.16 (0.23), residues: 438 loop : 0.18 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 208 HIS 0.009 0.002 HIS F 609 PHE 0.016 0.003 PHE C 228 TYR 0.018 0.003 TYR E 474 ARG 0.030 0.002 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASN cc_start: 0.7891 (m110) cc_final: 0.7669 (m-40) REVERT: A 21 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7096 (mtt-85) REVERT: A 34 GLU cc_start: 0.8172 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 156 ARG cc_start: 0.7471 (mtm110) cc_final: 0.7031 (mmt-90) REVERT: A 159 ASP cc_start: 0.8527 (m-30) cc_final: 0.8322 (m-30) REVERT: A 611 LYS cc_start: 0.8604 (mmpt) cc_final: 0.8403 (mmtp) REVERT: B 3 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7485 (tmm-80) REVERT: B 20 ASN cc_start: 0.7916 (m110) cc_final: 0.7638 (m-40) REVERT: B 21 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7237 (mtt-85) REVERT: B 34 GLU cc_start: 0.8199 (tt0) cc_final: 0.7939 (tm-30) REVERT: B 35 LEU cc_start: 0.8270 (mp) cc_final: 0.8014 (mp) REVERT: B 51 HIS cc_start: 0.7162 (t-90) cc_final: 0.6953 (t-90) REVERT: B 156 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7282 (mmt-90) REVERT: B 239 MET cc_start: 0.8984 (mmm) cc_final: 0.8681 (mmm) REVERT: B 263 GLN cc_start: 0.8609 (mt0) cc_final: 0.8408 (mt0) REVERT: B 591 MET cc_start: 0.9212 (mtp) cc_final: 0.8941 (mtp) REVERT: C 20 ASN cc_start: 0.7857 (m110) cc_final: 0.7654 (m-40) REVERT: C 21 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7243 (mtt-85) REVERT: C 34 GLU cc_start: 0.8161 (tt0) cc_final: 0.7942 (tm-30) REVERT: C 51 HIS cc_start: 0.7148 (t-90) cc_final: 0.6939 (t-90) REVERT: C 156 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7261 (mmt-90) REVERT: C 175 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7895 (mm-30) REVERT: C 239 MET cc_start: 0.9002 (mmm) cc_final: 0.8598 (mmm) REVERT: C 591 MET cc_start: 0.9185 (mtp) cc_final: 0.8893 (mtp) REVERT: D 21 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7206 (mtt-85) REVERT: D 34 GLU cc_start: 0.8180 (tt0) cc_final: 0.7859 (tm-30) REVERT: D 156 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6880 (mmp80) REVERT: D 171 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8152 (ttp-110) REVERT: D 239 MET cc_start: 0.8948 (mmm) cc_final: 0.8596 (mmm) REVERT: D 376 MET cc_start: 0.9261 (mmm) cc_final: 0.9007 (mmm) REVERT: D 571 ASP cc_start: 0.7632 (m-30) cc_final: 0.7379 (m-30) REVERT: D 574 MET cc_start: 0.9053 (tpp) cc_final: 0.8838 (tpp) REVERT: D 632 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7549 (tp30) REVERT: E 5 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.6927 (ttp-170) REVERT: E 20 ASN cc_start: 0.7973 (m110) cc_final: 0.7522 (m-40) REVERT: E 21 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7207 (mtt-85) REVERT: E 34 GLU cc_start: 0.8148 (tt0) cc_final: 0.7909 (tm-30) REVERT: E 156 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7214 (mmt-90) REVERT: E 159 ASP cc_start: 0.8472 (m-30) cc_final: 0.8237 (m-30) REVERT: E 239 MET cc_start: 0.9038 (mmm) cc_final: 0.8739 (mmm) REVERT: F 4 TYR cc_start: 0.8517 (m-80) cc_final: 0.8177 (m-80) REVERT: F 5 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.6869 (ttp-170) REVERT: F 20 ASN cc_start: 0.7919 (m110) cc_final: 0.7714 (m-40) REVERT: F 156 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7339 (mmt-90) REVERT: F 159 ASP cc_start: 0.8545 (m-30) cc_final: 0.8300 (m-30) REVERT: F 239 MET cc_start: 0.9016 (mmm) cc_final: 0.8810 (mmm) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 1.9213 time to fit residues: 1265.1577 Evaluate side-chains 433 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 84 GLN B 270 ASN B 625 ASN C 263 GLN C 270 ASN D 20 ASN D 263 GLN D 270 ASN D 400 ASN E 263 GLN E 270 ASN F 270 ASN F 400 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33072 Z= 0.252 Angle : 0.543 8.752 44922 Z= 0.271 Chirality : 0.042 0.224 4794 Planarity : 0.005 0.085 5844 Dihedral : 7.978 86.969 4434 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.26 % Allowed : 7.68 % Favored : 91.07 % 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: 1.17 (0.13), residues: 3960 helix: 1.49 (0.12), residues: 1770 sheet: -0.38 (0.22), residues: 444 loop : 0.51 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 498 HIS 0.004 0.001 HIS C 127 PHE 0.017 0.002 PHE F 386 TYR 0.016 0.002 TYR E 460 ARG 0.007 0.001 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 450 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7330 (tmm-80) REVERT: A 21 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7211 (mtt-85) REVERT: A 45 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 156 ARG cc_start: 0.7589 (mtm110) cc_final: 0.6965 (mmp80) REVERT: A 164 MET cc_start: 0.9076 (mmp) cc_final: 0.8833 (mmt) REVERT: A 653 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8308 (mtmp) REVERT: B 20 ASN cc_start: 0.8241 (m110) cc_final: 0.7888 (m-40) REVERT: B 21 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7349 (mtt-85) REVERT: B 34 GLU cc_start: 0.8308 (tt0) cc_final: 0.7988 (tm-30) REVERT: B 45 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 51 HIS cc_start: 0.7312 (t-90) cc_final: 0.7072 (t-90) REVERT: B 155 ASP cc_start: 0.8123 (m-30) cc_final: 0.7891 (m-30) REVERT: B 156 ARG cc_start: 0.7597 (mtm110) cc_final: 0.7253 (mmt-90) REVERT: B 239 MET cc_start: 0.9178 (mmm) cc_final: 0.8840 (mmm) REVERT: B 259 GLU cc_start: 0.8116 (tt0) cc_final: 0.7845 (pm20) REVERT: B 591 MET cc_start: 0.9195 (mtp) cc_final: 0.8943 (mtp) REVERT: C 20 ASN cc_start: 0.8210 (m110) cc_final: 0.7952 (m-40) REVERT: C 21 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7386 (mtt-85) REVERT: C 45 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 51 HIS cc_start: 0.7317 (t-90) cc_final: 0.7085 (t-90) REVERT: C 138 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (pt) REVERT: C 156 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7352 (mmt-90) REVERT: C 175 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7899 (mm-30) REVERT: C 239 MET cc_start: 0.9193 (mmm) cc_final: 0.8849 (mmm) REVERT: C 591 MET cc_start: 0.9180 (mtp) cc_final: 0.8870 (mtp) REVERT: C 633 LYS cc_start: 0.8724 (tttt) cc_final: 0.8505 (tttm) REVERT: D 3 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7396 (tmm-80) REVERT: D 21 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7380 (mtt-85) REVERT: D 34 GLU cc_start: 0.8266 (tt0) cc_final: 0.7891 (tm-30) REVERT: D 45 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 156 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6990 (mmp80) REVERT: D 164 MET cc_start: 0.9063 (mmp) cc_final: 0.8828 (mmt) REVERT: D 476 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: D 571 ASP cc_start: 0.7689 (m-30) cc_final: 0.7428 (m-30) REVERT: D 650 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: D 653 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8066 (mtmp) REVERT: E 68 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7072 (t70) REVERT: E 138 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8548 (pt) REVERT: E 156 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7244 (mmt-90) REVERT: E 159 ASP cc_start: 0.8559 (m-30) cc_final: 0.8286 (m-30) REVERT: E 239 MET cc_start: 0.9141 (mmm) cc_final: 0.8813 (mmm) REVERT: E 259 GLU cc_start: 0.8047 (tt0) cc_final: 0.7833 (pm20) REVERT: E 476 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: E 650 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: F 3 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7511 (tmm-80) REVERT: F 20 ASN cc_start: 0.8065 (m110) cc_final: 0.7826 (m-40) REVERT: F 159 ASP cc_start: 0.8656 (m-30) cc_final: 0.8398 (m-30) REVERT: F 239 MET cc_start: 0.9152 (mmm) cc_final: 0.8917 (mmm) REVERT: F 611 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8427 (mmtm) REVERT: F 650 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: F 653 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8250 (mtmp) outliers start: 43 outliers final: 14 residues processed: 477 average time/residue: 1.7763 time to fit residues: 974.0177 Evaluate side-chains 443 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 418 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 68 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 650 GLU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 chunk 299 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 389 optimal weight: 0.9980 chunk 320 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 263 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN B 625 ASN C 263 GLN C 270 ASN D 38 GLN D 263 GLN E 20 ASN E 38 GLN E 263 GLN E 270 ASN F 198 ASN F 263 GLN F 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33072 Z= 0.238 Angle : 0.532 10.091 44922 Z= 0.264 Chirality : 0.041 0.243 4794 Planarity : 0.005 0.078 5844 Dihedral : 7.879 85.562 4434 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.78 % Allowed : 8.46 % Favored : 89.75 % 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: 1.30 (0.13), residues: 3960 helix: 1.61 (0.12), residues: 1770 sheet: -0.44 (0.22), residues: 444 loop : 0.61 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.004 0.001 HIS E 127 PHE 0.014 0.002 PHE F 386 TYR 0.015 0.002 TYR F 460 ARG 0.006 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 426 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7325 (tmm-80) REVERT: A 21 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.7341 (mtt-85) REVERT: A 45 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 66 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8177 (ttm-80) REVERT: A 156 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7073 (mmt-90) REVERT: A 650 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: A 653 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8243 (mtmp) REVERT: B 20 ASN cc_start: 0.8421 (m110) cc_final: 0.8187 (m-40) REVERT: B 21 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7304 (mtt-85) REVERT: B 156 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7231 (mmt-90) REVERT: B 239 MET cc_start: 0.9191 (mmm) cc_final: 0.8868 (mmm) REVERT: B 259 GLU cc_start: 0.8119 (tt0) cc_final: 0.7853 (pm20) REVERT: B 591 MET cc_start: 0.9195 (mtp) cc_final: 0.8994 (mtp) REVERT: C 20 ASN cc_start: 0.8366 (m110) cc_final: 0.8084 (m-40) REVERT: C 21 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7326 (mtt-85) REVERT: C 45 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 51 HIS cc_start: 0.7371 (t-90) cc_final: 0.7150 (t-90) REVERT: C 138 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8558 (pt) REVERT: C 156 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7287 (mmt-90) REVERT: C 175 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7899 (mm-30) REVERT: C 239 MET cc_start: 0.9198 (mmm) cc_final: 0.8811 (mmm) REVERT: C 591 MET cc_start: 0.9182 (mtp) cc_final: 0.8892 (mtp) REVERT: C 621 LYS cc_start: 0.8558 (tmtm) cc_final: 0.8356 (tptt) REVERT: D 3 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7361 (tmm-80) REVERT: D 21 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7269 (mtt-85) REVERT: D 45 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7648 (mt-10) REVERT: D 66 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7929 (ttm-80) REVERT: D 156 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7048 (mmp80) REVERT: D 476 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: D 571 ASP cc_start: 0.7712 (m-30) cc_final: 0.7444 (m-30) REVERT: D 650 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: D 653 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8029 (mtmp) REVERT: E 3 ARG cc_start: 0.7935 (tmm-80) cc_final: 0.7658 (tmm-80) REVERT: E 5 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7787 (tpp-160) REVERT: E 66 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8167 (ttm-80) REVERT: E 138 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (pt) REVERT: E 156 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7259 (mmt-90) REVERT: E 159 ASP cc_start: 0.8576 (m-30) cc_final: 0.8303 (m-30) REVERT: E 239 MET cc_start: 0.9158 (mmm) cc_final: 0.8801 (mmm) REVERT: E 259 GLU cc_start: 0.8047 (tt0) cc_final: 0.7812 (pm20) REVERT: E 476 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: F 20 ASN cc_start: 0.8248 (m110) cc_final: 0.7967 (m-40) REVERT: F 159 ASP cc_start: 0.8667 (m-30) cc_final: 0.8428 (m-30) REVERT: F 239 MET cc_start: 0.9175 (mmm) cc_final: 0.8953 (mmm) REVERT: F 650 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: F 653 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8263 (mtmp) outliers start: 61 outliers final: 26 residues processed: 465 average time/residue: 1.7704 time to fit residues: 946.5531 Evaluate side-chains 450 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 411 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 342 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 270 ASN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN B 539 GLN C 263 GLN C 539 GLN D 84 GLN D 263 GLN E 38 GLN E 263 GLN E 270 ASN E 539 GLN F 198 ASN F 263 GLN F 270 ASN F 539 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33072 Z= 0.315 Angle : 0.563 7.767 44922 Z= 0.280 Chirality : 0.043 0.230 4794 Planarity : 0.005 0.093 5844 Dihedral : 7.913 85.178 4434 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 9.43 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.13), residues: 3960 helix: 1.57 (0.12), residues: 1770 sheet: -0.63 (0.20), residues: 474 loop : 0.71 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 208 HIS 0.005 0.001 HIS F 51 PHE 0.016 0.002 PHE B 482 TYR 0.017 0.002 TYR B 97 ARG 0.011 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 415 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7385 (tmm-80) REVERT: A 21 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7308 (mtt-85) REVERT: A 45 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 66 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (ttm-80) REVERT: A 156 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7024 (mmp80) REVERT: A 650 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: A 653 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8326 (mtmp) REVERT: B 21 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7309 (mtt-85) REVERT: B 45 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 156 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7239 (mmt-90) REVERT: B 239 MET cc_start: 0.9267 (mmm) cc_final: 0.9009 (mmm) REVERT: B 259 GLU cc_start: 0.8080 (tt0) cc_final: 0.7830 (pm20) REVERT: C 5 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7844 (tpp-160) REVERT: C 20 ASN cc_start: 0.8437 (m110) cc_final: 0.8214 (m-40) REVERT: C 21 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7364 (mtt-85) REVERT: C 45 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7568 (mt-10) REVERT: C 51 HIS cc_start: 0.7575 (t-90) cc_final: 0.7308 (t-90) REVERT: C 138 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8594 (pt) REVERT: C 156 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7258 (mmt-90) REVERT: C 175 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7912 (mm-30) REVERT: C 239 MET cc_start: 0.9286 (mmm) cc_final: 0.9038 (mmm) REVERT: C 591 MET cc_start: 0.9179 (mtp) cc_final: 0.8824 (mtp) REVERT: C 621 LYS cc_start: 0.8566 (tmtm) cc_final: 0.8340 (tptt) REVERT: D 3 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7420 (tmm-80) REVERT: D 21 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7303 (mtt-85) REVERT: D 45 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7701 (mt-10) REVERT: D 66 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7929 (ttm-80) REVERT: D 131 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: D 156 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7096 (mmp80) REVERT: D 650 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: E 3 ARG cc_start: 0.7899 (tmm-80) cc_final: 0.7636 (tmm-80) REVERT: E 66 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8101 (ttm-80) REVERT: E 138 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8514 (pt) REVERT: E 156 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7315 (mmt-90) REVERT: E 159 ASP cc_start: 0.8603 (m-30) cc_final: 0.8339 (m-30) REVERT: E 239 MET cc_start: 0.9233 (mmm) cc_final: 0.8892 (mmm) REVERT: F 20 ASN cc_start: 0.8509 (m110) cc_final: 0.8232 (m-40) REVERT: F 650 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: F 653 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8284 (mtmp) outliers start: 54 outliers final: 29 residues processed: 448 average time/residue: 1.7519 time to fit residues: 903.4328 Evaluate side-chains 441 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 401 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 326 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 84 GLN B 263 GLN B 270 ASN C 84 GLN D 84 GLN D 198 ASN D 263 GLN D 539 GLN E 270 ASN F 198 ASN F 263 GLN F 270 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33072 Z= 0.283 Angle : 0.545 7.960 44922 Z= 0.270 Chirality : 0.042 0.223 4794 Planarity : 0.005 0.105 5844 Dihedral : 7.821 85.175 4434 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.66 % Allowed : 10.01 % Favored : 88.32 % 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: 1.29 (0.13), residues: 3960 helix: 1.62 (0.12), residues: 1764 sheet: -0.67 (0.20), residues: 474 loop : 0.68 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 208 HIS 0.007 0.001 HIS F 51 PHE 0.014 0.002 PHE B 482 TYR 0.016 0.002 TYR E 460 ARG 0.006 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 403 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7440 (tmm-80) REVERT: A 21 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7318 (mtt-85) REVERT: A 45 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 156 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7057 (mmp80) REVERT: A 653 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8296 (mtmp) REVERT: B 21 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7340 (mtt-85) REVERT: B 45 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 156 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7217 (mmt-90) REVERT: B 239 MET cc_start: 0.9254 (mmm) cc_final: 0.9028 (mmm) REVERT: B 259 GLU cc_start: 0.8059 (tt0) cc_final: 0.7839 (pm20) REVERT: B 653 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: C 20 ASN cc_start: 0.8440 (m110) cc_final: 0.8227 (m-40) REVERT: C 21 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7355 (mtt-85) REVERT: C 45 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 51 HIS cc_start: 0.7596 (t-90) cc_final: 0.7355 (t-90) REVERT: C 138 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8601 (pt) REVERT: C 156 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7145 (mmp80) REVERT: C 175 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7910 (mm-30) REVERT: C 239 MET cc_start: 0.9251 (mmm) cc_final: 0.8965 (mmm) REVERT: C 591 MET cc_start: 0.9193 (mtp) cc_final: 0.8871 (mtp) REVERT: C 621 LYS cc_start: 0.8574 (tmtm) cc_final: 0.8337 (tptt) REVERT: C 653 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8442 (mtmm) REVERT: D 3 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7425 (tmm-80) REVERT: D 21 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7299 (mtt-85) REVERT: D 45 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 66 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: D 156 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7086 (mmp80) REVERT: D 650 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: E 3 ARG cc_start: 0.7897 (tmm-80) cc_final: 0.7652 (tmm-80) REVERT: E 38 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8167 (mm-40) REVERT: E 66 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8038 (ttm-80) REVERT: E 138 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8512 (pt) REVERT: E 156 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7287 (mmt-90) REVERT: E 159 ASP cc_start: 0.8599 (m-30) cc_final: 0.8339 (m-30) REVERT: E 239 MET cc_start: 0.9199 (mmm) cc_final: 0.8852 (mmm) REVERT: F 20 ASN cc_start: 0.8541 (m110) cc_final: 0.8289 (m-40) REVERT: F 45 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7671 (mt-10) REVERT: F 650 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: F 653 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8272 (mtmp) outliers start: 57 outliers final: 32 residues processed: 442 average time/residue: 1.7560 time to fit residues: 893.1547 Evaluate side-chains 436 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 394 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 270 ASN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN B 270 ASN C 263 GLN D 38 GLN D 84 GLN D 198 ASN D 263 GLN D 270 ASN D 484 GLN E 263 GLN E 270 ASN F 198 ASN F 263 GLN F 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 33072 Z= 0.424 Angle : 0.610 8.347 44922 Z= 0.302 Chirality : 0.045 0.221 4794 Planarity : 0.006 0.109 5844 Dihedral : 7.977 85.195 4434 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.93 % Allowed : 10.10 % Favored : 87.97 % 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: 1.19 (0.13), residues: 3960 helix: 1.44 (0.12), residues: 1782 sheet: -0.65 (0.20), residues: 474 loop : 0.73 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 208 HIS 0.007 0.001 HIS F 51 PHE 0.019 0.002 PHE B 482 TYR 0.020 0.002 TYR D 97 ARG 0.006 0.000 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 402 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.7416 (tmm-80) REVERT: A 21 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7313 (mtt-85) REVERT: A 45 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 119 ASN cc_start: 0.9020 (t0) cc_final: 0.8804 (t0) REVERT: A 156 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7097 (mmp80) REVERT: A 653 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8361 (mtmp) REVERT: B 21 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7308 (mtt-85) REVERT: B 45 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 156 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7247 (mmt-90) REVERT: B 259 GLU cc_start: 0.8036 (tt0) cc_final: 0.7714 (pm20) REVERT: B 653 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: C 20 ASN cc_start: 0.8471 (m110) cc_final: 0.8249 (m-40) REVERT: C 21 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7360 (mtt-85) REVERT: C 45 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7712 (mt-10) REVERT: C 138 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8626 (pt) REVERT: C 156 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7141 (mmp80) REVERT: C 591 MET cc_start: 0.9189 (mtp) cc_final: 0.8894 (mtp) REVERT: C 653 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8472 (mtmm) REVERT: D 21 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7293 (mtt-85) REVERT: D 45 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7763 (mt-10) REVERT: D 66 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: D 156 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7095 (mmp80) REVERT: D 650 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: E 66 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8083 (ttm-80) REVERT: E 138 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8557 (pt) REVERT: E 156 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7237 (mmt-90) REVERT: E 159 ASP cc_start: 0.8606 (m-30) cc_final: 0.8342 (m-30) REVERT: E 239 MET cc_start: 0.9309 (mmm) cc_final: 0.8959 (mmm) REVERT: F 20 ASN cc_start: 0.8577 (m110) cc_final: 0.8366 (m-40) REVERT: F 650 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8236 (mm-30) REVERT: F 653 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8306 (mtmp) outliers start: 66 outliers final: 32 residues processed: 444 average time/residue: 1.8438 time to fit residues: 937.1453 Evaluate side-chains 438 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 396 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 216 optimal weight: 0.6980 chunk 322 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 chunk 381 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 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 263 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN C 84 GLN D 38 GLN D 84 GLN D 198 ASN D 263 GLN E 270 ASN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33072 Z= 0.171 Angle : 0.511 10.815 44922 Z= 0.252 Chirality : 0.039 0.194 4794 Planarity : 0.005 0.114 5844 Dihedral : 7.661 85.461 4434 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.52 % Allowed : 11.00 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.13), residues: 3960 helix: 1.73 (0.12), residues: 1764 sheet: -0.67 (0.21), residues: 468 loop : 0.67 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 208 HIS 0.006 0.001 HIS F 51 PHE 0.011 0.001 PHE B 482 TYR 0.013 0.001 TYR C 474 ARG 0.010 0.000 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 406 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7433 (tmm-80) REVERT: A 21 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7358 (mtt-85) REVERT: A 45 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 156 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7089 (mmp80) REVERT: A 653 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8244 (mtmp) REVERT: B 21 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7322 (mtt-85) REVERT: B 45 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 66 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8311 (ttm-80) REVERT: B 156 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7230 (mmt-90) REVERT: B 259 GLU cc_start: 0.8026 (tt0) cc_final: 0.7717 (pm20) REVERT: C 20 ASN cc_start: 0.8448 (m110) cc_final: 0.8246 (m-40) REVERT: C 21 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7331 (mtt-85) REVERT: C 45 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 51 HIS cc_start: 0.7434 (t-90) cc_final: 0.7175 (t-90) REVERT: C 156 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7129 (mmp80) REVERT: D 3 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.7574 (tmm-80) REVERT: D 21 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7305 (mtt-85) REVERT: D 45 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7687 (mt-10) REVERT: D 156 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7067 (mmp80) REVERT: D 476 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: D 650 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: E 5 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7528 (tpt-90) REVERT: E 21 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7513 (mpt180) REVERT: E 66 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7914 (ttm-80) REVERT: E 138 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8422 (pp) REVERT: E 156 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7250 (mmt-90) REVERT: E 159 ASP cc_start: 0.8588 (m-30) cc_final: 0.8334 (m-30) REVERT: E 239 MET cc_start: 0.9100 (mmm) cc_final: 0.8799 (mmm) REVERT: E 476 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: F 20 ASN cc_start: 0.8537 (m110) cc_final: 0.8290 (m-40) REVERT: F 45 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7667 (mt-10) REVERT: F 66 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8109 (ttm-80) REVERT: F 476 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: F 650 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: F 653 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8227 (mtmp) outliers start: 52 outliers final: 23 residues processed: 438 average time/residue: 1.7838 time to fit residues: 898.0502 Evaluate side-chains 429 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 395 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 613 LYS Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 188 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN C 84 GLN C 263 GLN C 270 ASN C 484 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 263 GLN E 270 ASN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33072 Z= 0.205 Angle : 0.512 7.923 44922 Z= 0.254 Chirality : 0.040 0.201 4794 Planarity : 0.005 0.111 5844 Dihedral : 7.607 84.942 4434 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.23 % Allowed : 11.82 % Favored : 86.95 % 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: 1.40 (0.13), residues: 3960 helix: 1.77 (0.12), residues: 1764 sheet: -0.66 (0.21), residues: 468 loop : 0.68 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 498 HIS 0.006 0.001 HIS F 51 PHE 0.011 0.001 PHE C 482 TYR 0.013 0.002 TYR F 460 ARG 0.008 0.000 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 392 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7442 (tmm-80) REVERT: A 21 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7363 (mtt-85) REVERT: A 45 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 156 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7057 (mmp80) REVERT: A 653 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8224 (mtmp) REVERT: B 21 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7330 (mtt-85) REVERT: B 45 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 156 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7238 (mmt-90) REVERT: B 259 GLU cc_start: 0.8003 (tt0) cc_final: 0.7715 (pm20) REVERT: C 20 ASN cc_start: 0.8453 (m110) cc_final: 0.8164 (m-40) REVERT: C 21 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7338 (mtt-85) REVERT: C 45 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 51 HIS cc_start: 0.7232 (t-90) cc_final: 0.6982 (t-90) REVERT: C 156 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7114 (mmp80) REVERT: D 21 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7305 (mtt-85) REVERT: D 45 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 156 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7094 (mmp80) REVERT: D 650 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: E 5 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7537 (tpt-90) REVERT: E 66 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: E 138 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8448 (pp) REVERT: E 156 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7269 (mmt-90) REVERT: E 159 ASP cc_start: 0.8596 (m-30) cc_final: 0.8343 (m-30) REVERT: E 239 MET cc_start: 0.9149 (mmm) cc_final: 0.8835 (mmm) REVERT: E 476 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: F 20 ASN cc_start: 0.8542 (m110) cc_final: 0.8305 (m-40) REVERT: F 45 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7696 (mt-10) REVERT: F 66 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8096 (ttm-80) REVERT: F 476 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: F 650 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: F 653 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8177 (mtmp) outliers start: 42 outliers final: 21 residues processed: 421 average time/residue: 1.8386 time to fit residues: 887.9181 Evaluate side-chains 420 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 390 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 355 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33072 Z= 0.252 Angle : 0.532 8.335 44922 Z= 0.263 Chirality : 0.041 0.203 4794 Planarity : 0.005 0.102 5844 Dihedral : 7.604 84.776 4434 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.20 % Allowed : 11.85 % Favored : 86.95 % 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: 1.39 (0.13), residues: 3960 helix: 1.74 (0.12), residues: 1764 sheet: -0.60 (0.21), residues: 468 loop : 0.68 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.006 0.001 HIS F 51 PHE 0.012 0.002 PHE B 482 TYR 0.015 0.002 TYR C 460 ARG 0.008 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 396 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7465 (tmm-80) REVERT: A 21 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7364 (mtt-85) REVERT: A 45 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 156 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7049 (mmp80) REVERT: A 653 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8238 (mtmp) REVERT: B 21 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7323 (mtt-85) REVERT: B 45 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 156 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7241 (mmt-90) REVERT: B 259 GLU cc_start: 0.8003 (tt0) cc_final: 0.7713 (pm20) REVERT: B 653 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: C 20 ASN cc_start: 0.8463 (m110) cc_final: 0.8225 (m-40) REVERT: C 21 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7320 (mtt-85) REVERT: C 45 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 156 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7122 (mmp80) REVERT: D 21 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7307 (mtt-85) REVERT: D 45 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 156 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7083 (mmp80) REVERT: D 476 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 650 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8081 (mm-30) REVERT: E 5 ARG cc_start: 0.7899 (tpp-160) cc_final: 0.7445 (tpt-90) REVERT: E 21 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7497 (mpt180) REVERT: E 66 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7923 (ttm-80) REVERT: E 138 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8445 (pp) REVERT: E 156 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7271 (mmt-90) REVERT: E 159 ASP cc_start: 0.8595 (m-30) cc_final: 0.8342 (m-30) REVERT: E 239 MET cc_start: 0.9193 (mmm) cc_final: 0.8861 (mmm) REVERT: E 476 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: F 20 ASN cc_start: 0.8553 (m110) cc_final: 0.8318 (m-40) REVERT: F 45 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7706 (mt-10) REVERT: F 66 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8104 (ttm-80) REVERT: F 476 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: F 650 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: F 653 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8193 (mtmp) outliers start: 41 outliers final: 25 residues processed: 423 average time/residue: 1.8275 time to fit residues: 894.8720 Evaluate side-chains 428 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 392 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 4.9990 chunk 376 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 242 optimal weight: 0.4980 chunk 192 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN B 484 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33072 Z= 0.247 Angle : 0.534 9.075 44922 Z= 0.264 Chirality : 0.041 0.205 4794 Planarity : 0.005 0.102 5844 Dihedral : 7.570 84.802 4434 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.20 % Allowed : 12.03 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 3960 helix: 1.73 (0.12), residues: 1764 sheet: -0.58 (0.21), residues: 468 loop : 0.69 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.006 0.001 HIS F 51 PHE 0.012 0.002 PHE B 482 TYR 0.015 0.002 TYR C 460 ARG 0.009 0.000 ARG D 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 395 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7452 (tmm-80) REVERT: A 21 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7372 (mtt-85) REVERT: A 45 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 119 ASN cc_start: 0.9024 (t0) cc_final: 0.8778 (t0) REVERT: A 156 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7066 (mmp80) REVERT: A 653 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8244 (mtmp) REVERT: B 21 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7340 (mtt-85) REVERT: B 45 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 156 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7239 (mmt-90) REVERT: B 259 GLU cc_start: 0.7996 (tt0) cc_final: 0.7714 (pm20) REVERT: B 653 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: C 20 ASN cc_start: 0.8468 (m110) cc_final: 0.8167 (m-40) REVERT: C 21 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7334 (mtt-85) REVERT: C 45 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 156 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7120 (mmp80) REVERT: D 21 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7308 (mtt-85) REVERT: D 45 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7700 (mt-10) REVERT: D 156 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7080 (mmp80) REVERT: D 476 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: D 650 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: E 5 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7411 (tpt-90) REVERT: E 21 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7505 (mpt180) REVERT: E 66 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: E 138 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8444 (pp) REVERT: E 156 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7269 (mmt-90) REVERT: E 159 ASP cc_start: 0.8595 (m-30) cc_final: 0.8342 (m-30) REVERT: E 239 MET cc_start: 0.9191 (mmm) cc_final: 0.8856 (mmm) REVERT: E 476 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: F 20 ASN cc_start: 0.8555 (m110) cc_final: 0.8348 (m-40) REVERT: F 45 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7714 (mt-10) REVERT: F 66 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8100 (ttm-80) REVERT: F 476 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: F 650 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: F 653 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8198 (mtmp) outliers start: 41 outliers final: 24 residues processed: 423 average time/residue: 1.8225 time to fit residues: 888.3961 Evaluate side-chains 429 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 394 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 636 LYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 289 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 1.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094543 restraints weight = 34946.040| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.80 r_work: 0.3151 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33072 Z= 0.214 Angle : 0.518 8.083 44922 Z= 0.257 Chirality : 0.040 0.207 4794 Planarity : 0.005 0.098 5844 Dihedral : 7.413 84.672 4434 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.26 % Allowed : 11.85 % Favored : 86.89 % 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: 1.42 (0.13), residues: 3960 helix: 1.77 (0.12), residues: 1764 sheet: -0.56 (0.21), residues: 468 loop : 0.69 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 498 HIS 0.006 0.001 HIS F 51 PHE 0.011 0.001 PHE B 482 TYR 0.014 0.002 TYR F 460 ARG 0.009 0.000 ARG E 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13665.02 seconds wall clock time: 242 minutes 7.35 seconds (14527.35 seconds total)