Starting phenix.real_space_refine on Mon Mar 18 21:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghe_40042/03_2024/8ghe_40042_updated.pdb" } resolution = 2.05 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= 0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 3 5.49 5 S 137 5.16 5 C 13637 2.51 5 N 3721 2.21 5 O 4691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22193 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 5327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 5434 Chain: "C" Number of atoms: 5319 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 5443 Chain: "D" Number of atoms: 5319 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 5443 Chain: "A" Number of atoms: 5327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 5434 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'3VV': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Classifications: {'water': 197} Link IDs: {None: 196} Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 212 Classifications: {'water': 212} Link IDs: {None: 211} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 198 Classifications: {'water': 198} Link IDs: {None: 197} Chain: "A" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Time building chain proxies: 21.35, per 1000 atoms: 0.96 Number of scatterers: 22193 At special positions: 0 Unit cell: (109.06, 113.98, 148.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 137 16.00 P 3 15.00 O 4691 8.00 N 3721 7.00 C 13637 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: 9.78 Conformation dependent library (CDL) restraints added in 7.5 seconds 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 16 sheets defined 42.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.505A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) 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 191 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: 4.395A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.225A 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 389 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.747A 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 443 through 449 removed outlier: 3.783A pdb=" N ALA B 448 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 482 removed outlier: 3.639A pdb=" N LEU B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) 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: 3.974A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.502A pdb=" N GLN C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) 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 191 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: 4.371A pdb=" N PHE C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.178A 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 389 Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 443 through 449 removed outlier: 3.833A pdb=" N ALA C 448 " --> pdb=" O PRO C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 482 removed outlier: 3.626A pdb=" N LEU C 481 " --> pdb=" O GLY C 477 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) 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: 3.988A pdb=" N GLN C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.562A pdb=" N GLN D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) 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 191 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: 4.396A pdb=" N PHE D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 4.250A 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 389 Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 443 through 449 removed outlier: 3.774A pdb=" N ALA D 448 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 482 removed outlier: 3.609A pdb=" N LEU D 481 " --> pdb=" O GLY D 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) 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: 3.966A pdb=" N GLN D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) 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 191 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: 4.142A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.044A 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 Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 443 through 450 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 510 through 513 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: 3.942A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.501A pdb=" N ARG B 80 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.578A pdb=" N ALA B 12 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 32 through 39 removed outlier: 4.433A pdb=" N ARG B 21 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.071A pdb=" N LYS B 304 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.504A pdb=" N ARG C 80 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.608A pdb=" N ALA C 12 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 32 through 39 Processing sheet with id= H, first strand: chain 'C' and resid 273 through 277 removed outlier: 5.939A pdb=" N LYS C 304 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 47 through 52 Processing sheet with id= J, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.518A pdb=" N ALA D 12 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 32 through 39 removed outlier: 4.544A pdb=" N ARG D 21 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 273 through 277 removed outlier: 5.971A pdb=" N LYS D 304 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 47 through 52 Processing sheet with id= N, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= O, first strand: chain 'A' and resid 32 through 39 Processing sheet with id= P, first strand: chain 'A' and resid 273 through 277 removed outlier: 5.804A pdb=" N LYS A 304 " --> pdb=" O PRO A 313 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 10.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4179 1.33 - 1.45: 5350 1.45 - 1.57: 12191 1.57 - 1.69: 5 1.69 - 1.82: 206 Bond restraints: 21931 Sorted by residual: bond pdb=" C49 3VV A 702 " pdb=" C50 3VV A 702 " ideal model delta sigma weight residual 1.291 1.529 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C49 3VV A 702 " pdb=" O48 3VV A 702 " ideal model delta sigma weight residual 1.621 1.420 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C47 3VV A 702 " pdb=" O48 3VV A 702 " ideal model delta sigma weight residual 1.286 1.445 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" C24 3VV A 702 " pdb=" N23 3VV A 702 " ideal model delta sigma weight residual 1.474 1.334 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C29 3VV A 702 " pdb=" N28 3VV A 702 " ideal model delta sigma weight residual 1.469 1.331 0.138 2.00e-02 2.50e+03 4.78e+01 ... (remaining 21926 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.72: 649 105.72 - 113.05: 11643 113.05 - 120.38: 8665 120.38 - 127.71: 8543 127.71 - 135.04: 321 Bond angle restraints: 29821 Sorted by residual: angle pdb=" C09 3VV A 702 " pdb=" C10 3VV A 702 " pdb=" C11 3VV A 702 " ideal model delta sigma weight residual 152.65 127.57 25.08 3.00e+00 1.11e-01 6.99e+01 angle pdb=" N63 3VV A 702 " pdb=" C62 3VV A 702 " pdb=" N64 3VV A 702 " ideal model delta sigma weight residual 103.64 118.49 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C08 3VV A 702 " pdb=" C09 3VV A 702 " pdb=" C10 3VV A 702 " ideal model delta sigma weight residual 112.20 125.99 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 122.69 -4.76 1.20e+00 6.94e-01 1.57e+01 angle pdb=" C61 3VV A 702 " pdb=" C62 3VV A 702 " pdb=" N63 3VV A 702 " ideal model delta sigma weight residual 134.98 123.80 11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 29816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 12934 31.13 - 62.26: 229 62.26 - 93.38: 26 93.38 - 124.51: 1 124.51 - 155.64: 1 Dihedral angle restraints: 13191 sinusoidal: 5471 harmonic: 7720 Sorted by residual: dihedral pdb=" CD AARG B 585 " pdb=" NE AARG B 585 " pdb=" CZ AARG B 585 " pdb=" NH1AARG B 585 " ideal model delta sinusoidal sigma weight residual 0.00 -62.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" C09 3VV A 702 " pdb=" C10 3VV A 702 " pdb=" C11 3VV A 702 " pdb=" C12 3VV A 702 " ideal model delta sinusoidal sigma weight residual 90.40 -65.24 155.64 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CD BARG B 585 " pdb=" NE BARG B 585 " pdb=" CZ BARG B 585 " pdb=" NH1BARG B 585 " ideal model delta sinusoidal sigma weight residual 0.00 -34.37 34.37 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 13188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2869 0.073 - 0.147: 308 0.147 - 0.220: 21 0.220 - 0.293: 8 0.293 - 0.367: 1 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C50 3VV A 702 " pdb=" C49 3VV A 702 " pdb=" C52 3VV A 702 " pdb=" O51 3VV A 702 " both_signs ideal model delta sigma weight residual False -2.38 -2.75 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE A 390 " pdb=" CA ILE A 390 " pdb=" CG1 ILE A 390 " pdb=" CG2 ILE A 390 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+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 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3204 not shown) Planarity restraints: 3877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD AARG B 585 " 0.796 9.50e-02 1.11e+02 3.58e-01 8.65e+01 pdb=" NE AARG B 585 " -0.067 2.00e-02 2.50e+03 pdb=" CZ AARG B 585 " 0.042 2.00e-02 2.50e+03 pdb=" NH1AARG B 585 " -0.015 2.00e-02 2.50e+03 pdb=" NH2AARG B 585 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD BARG B 585 " 0.486 9.50e-02 1.11e+02 2.19e-01 3.50e+01 pdb=" NE BARG B 585 " -0.044 2.00e-02 2.50e+03 pdb=" CZ BARG B 585 " 0.036 2.00e-02 2.50e+03 pdb=" NH1BARG B 585 " -0.017 2.00e-02 2.50e+03 pdb=" NH2BARG B 585 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 444 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C PRO A 444 " 0.060 2.00e-02 2.50e+03 pdb=" O PRO A 444 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 445 " -0.020 2.00e-02 2.50e+03 ... (remaining 3874 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3929 2.76 - 3.30: 21687 3.30 - 3.83: 45437 3.83 - 4.37: 53305 4.37 - 4.90: 84383 Nonbonded interactions: 208741 Sorted by model distance: nonbonded pdb=" NE2 HIS C 360 " pdb="FE FE2 C 701 " model vdw 2.229 3.080 nonbonded pdb=" NE2 HIS D 360 " pdb="FE FE2 D 701 " model vdw 2.230 3.080 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 701 " model vdw 2.230 3.080 nonbonded pdb=" NE2 HIS B 360 " pdb="FE FE2 B 701 " model vdw 2.230 3.080 nonbonded pdb=" NE2 HIS B 365 " pdb="FE FE2 B 701 " model vdw 2.233 3.080 ... (remaining 208736 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' and (resid 2 through 188 or resid 190 through 499 or resid 501 throug \ h 584 or resid 586 through 663 or resid 701)) selection = (chain 'B' and (resid 2 through 188 or resid 190 through 499 or resid 501 throug \ h 584 or resid 586 through 663 or resid 701)) selection = (chain 'C' and (resid 2 through 188 or resid 190 through 499 or resid 501 throug \ h 584 or resid 586 through 663 or resid 701)) selection = (chain 'D' and (resid 2 through 188 or resid 190 through 499 or resid 501 throug \ h 584 or resid 586 through 663 or resid 701)) } 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=0.42 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.220 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 75.040 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.006 0.238 21931 Z= 0.384 Angle : 0.728 25.084 29821 Z= 0.374 Chirality : 0.048 0.367 3207 Planarity : 0.009 0.358 3877 Dihedral : 12.122 155.639 8195 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.04 % Allowed : 2.27 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 2646 helix: -1.03 (0.12), residues: 1122 sheet: -0.49 (0.23), residues: 316 loop : 0.14 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 208 HIS 0.005 0.001 HIS A 540 PHE 0.023 0.002 PHE C 414 TYR 0.022 0.002 TYR A 474 ARG 0.016 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8230 (mt0) cc_final: 0.7381 (mp10) REVERT: B 35 LEU cc_start: 0.7562 (mp) cc_final: 0.7134 (tt) REVERT: B 64 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.7169 (ttm110) REVERT: B 91 GLU cc_start: 0.8009 (pt0) cc_final: 0.7754 (pm20) REVERT: B 130 LYS cc_start: 0.8729 (tttm) cc_final: 0.8350 (tmmt) REVERT: B 133 LYS cc_start: 0.8801 (mttp) cc_final: 0.8491 (mmmt) REVERT: B 137 GLN cc_start: 0.8388 (mm110) cc_final: 0.8007 (mm-40) REVERT: B 210 GLN cc_start: 0.8249 (mt0) cc_final: 0.7782 (pt0) REVERT: B 216 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 226 GLU cc_start: 0.8156 (pm20) cc_final: 0.7938 (tm-30) REVERT: B 310 LYS cc_start: 0.8473 (mttm) cc_final: 0.8253 (mtpt) REVERT: B 314 MET cc_start: 0.9004 (mtp) cc_final: 0.8784 (mtp) REVERT: B 439 CYS cc_start: 0.8474 (p) cc_final: 0.7929 (t) REVERT: B 578 MET cc_start: 0.9360 (mmm) cc_final: 0.9082 (mmm) REVERT: B 593 ILE cc_start: 0.9059 (mm) cc_final: 0.8799 (mt) REVERT: C 6 ILE cc_start: 0.8578 (mp) cc_final: 0.8211 (mm) REVERT: C 46 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 91 GLU cc_start: 0.8207 (pt0) cc_final: 0.7986 (pm20) REVERT: C 175 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8663 (mt-10) REVERT: C 226 GLU cc_start: 0.8077 (pm20) cc_final: 0.7865 (mp0) REVERT: C 439 CYS cc_start: 0.8472 (m) cc_final: 0.7987 (t) REVERT: C 568 THR cc_start: 0.8752 (m) cc_final: 0.7357 (p) REVERT: D 91 GLU cc_start: 0.8290 (pt0) cc_final: 0.7737 (pm20) REVERT: D 107 SER cc_start: 0.8981 (m) cc_final: 0.8773 (t) REVERT: D 263 GLN cc_start: 0.8700 (mt0) cc_final: 0.8461 (mt0) REVERT: D 435 GLN cc_start: 0.8727 (mt0) cc_final: 0.8434 (mm110) REVERT: D 449 ASP cc_start: 0.8408 (t70) cc_final: 0.8085 (t0) REVERT: D 568 THR cc_start: 0.8779 (m) cc_final: 0.8487 (p) REVERT: D 613 LYS cc_start: 0.8746 (mttp) cc_final: 0.8536 (mttp) REVERT: A 5 ARG cc_start: 0.7282 (tpp80) cc_final: 0.6662 (ttm-80) REVERT: A 6 ILE cc_start: 0.8221 (mp) cc_final: 0.7951 (mt) REVERT: A 14 LEU cc_start: 0.9217 (tp) cc_final: 0.8990 (tm) REVERT: A 23 GLN cc_start: 0.8313 (mt0) cc_final: 0.7953 (mt0) REVERT: A 61 GLN cc_start: 0.7969 (mt0) cc_final: 0.7458 (mt0) REVERT: A 159 ASP cc_start: 0.8528 (m-30) cc_final: 0.8264 (m-30) REVERT: A 504 GLU cc_start: 0.8127 (tp30) cc_final: 0.7630 (tp30) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.5390 time to fit residues: 640.7959 Evaluate side-chains 238 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.0970 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 435 GLN B 625 ASN C 51 HIS ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 644 GLN A 20 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 520 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21931 Z= 0.237 Angle : 0.539 8.455 29821 Z= 0.274 Chirality : 0.040 0.251 3207 Planarity : 0.005 0.054 3877 Dihedral : 6.450 150.503 2935 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 8.09 % Favored : 90.55 % 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: 0.74 (0.15), residues: 2646 helix: 0.95 (0.14), residues: 1134 sheet: -0.59 (0.23), residues: 328 loop : 0.58 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 176 HIS 0.005 0.001 HIS C 127 PHE 0.025 0.001 PHE D 49 TYR 0.017 0.002 TYR C 460 ARG 0.010 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8000 (mt0) cc_final: 0.7482 (mt0) REVERT: B 91 GLU cc_start: 0.8098 (pt0) cc_final: 0.7800 (pm20) REVERT: B 126 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8714 (mttm) REVERT: B 133 LYS cc_start: 0.8783 (mttp) cc_final: 0.8476 (mmmt) REVERT: B 137 GLN cc_start: 0.8438 (mm110) cc_final: 0.7976 (mm-40) REVERT: B 210 GLN cc_start: 0.8157 (mt0) cc_final: 0.7867 (pt0) REVERT: B 314 MET cc_start: 0.8968 (mtp) cc_final: 0.8700 (mtp) REVERT: B 439 CYS cc_start: 0.8655 (p) cc_final: 0.8167 (t) REVERT: C 66 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6976 (ttp80) REVERT: C 578 MET cc_start: 0.9330 (mmm) cc_final: 0.9121 (mmm) REVERT: D 35 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7901 (tt) REVERT: D 91 GLU cc_start: 0.8305 (pt0) cc_final: 0.7693 (pm20) REVERT: D 263 GLN cc_start: 0.8692 (mt0) cc_final: 0.8273 (mt0) REVERT: D 435 GLN cc_start: 0.8686 (mt0) cc_final: 0.8300 (mm110) REVERT: D 449 ASP cc_start: 0.8183 (t70) cc_final: 0.7783 (t0) REVERT: D 568 THR cc_start: 0.8840 (m) cc_final: 0.8470 (p) REVERT: D 613 LYS cc_start: 0.8825 (mttp) cc_final: 0.8603 (mttp) REVERT: A 5 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7740 (ttm-80) REVERT: A 7 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7917 (ttm110) REVERT: A 23 GLN cc_start: 0.8328 (mt0) cc_final: 0.7935 (mt0) REVERT: A 34 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 61 GLN cc_start: 0.7988 (mt0) cc_final: 0.7518 (mt0) REVERT: A 114 ARG cc_start: 0.8625 (mtt90) cc_final: 0.8211 (mtt90) outliers start: 30 outliers final: 8 residues processed: 264 average time/residue: 1.5009 time to fit residues: 448.3968 Evaluate side-chains 231 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 435 GLN B 625 ASN C 69 HIS ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 269 GLN A 522 GLN A 626 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 21931 Z= 0.469 Angle : 0.636 9.487 29821 Z= 0.319 Chirality : 0.045 0.254 3207 Planarity : 0.005 0.052 3877 Dihedral : 6.579 147.585 2935 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 9.54 % Favored : 89.28 % 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: 1.20 (0.16), residues: 2646 helix: 1.44 (0.14), residues: 1158 sheet: -0.53 (0.24), residues: 328 loop : 0.74 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 70 HIS 0.005 0.001 HIS A 609 PHE 0.020 0.002 PHE B 386 TYR 0.021 0.002 TYR C 551 ARG 0.010 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7743 (ttp80) REVERT: B 23 GLN cc_start: 0.8109 (mt0) cc_final: 0.7830 (mt0) REVERT: B 35 LEU cc_start: 0.7935 (mp) cc_final: 0.7674 (tt) REVERT: B 64 ARG cc_start: 0.7109 (ttp-110) cc_final: 0.6891 (ttm110) REVERT: B 91 GLU cc_start: 0.8015 (pt0) cc_final: 0.7774 (pm20) REVERT: B 126 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8700 (ptpp) REVERT: B 210 GLN cc_start: 0.8224 (mt0) cc_final: 0.7887 (pt0) REVERT: B 439 CYS cc_start: 0.8679 (p) cc_final: 0.8212 (t) REVERT: C 66 ARG cc_start: 0.7348 (ttp80) cc_final: 0.7130 (ttp80) REVERT: D 35 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7685 (mp) REVERT: D 91 GLU cc_start: 0.8335 (pt0) cc_final: 0.7749 (pm20) REVERT: D 126 LYS cc_start: 0.8736 (mtmp) cc_final: 0.8472 (ptpt) REVERT: D 435 GLN cc_start: 0.8743 (mt0) cc_final: 0.8366 (mm110) REVERT: D 449 ASP cc_start: 0.8684 (t70) cc_final: 0.8425 (t0) REVERT: D 568 THR cc_start: 0.8910 (m) cc_final: 0.8468 (p) REVERT: A 23 GLN cc_start: 0.8409 (mt0) cc_final: 0.7852 (mt0) REVERT: A 34 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 61 GLN cc_start: 0.8062 (mt0) cc_final: 0.7565 (mt0) outliers start: 26 outliers final: 12 residues processed: 240 average time/residue: 1.4745 time to fit residues: 401.4954 Evaluate side-chains 223 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 249 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 263 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21931 Z= 0.284 Angle : 0.560 8.794 29821 Z= 0.279 Chirality : 0.041 0.249 3207 Planarity : 0.005 0.048 3877 Dihedral : 6.355 147.747 2935 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 9.76 % Favored : 88.93 % 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 (0.16), residues: 2646 helix: 1.70 (0.15), residues: 1158 sheet: -0.54 (0.24), residues: 328 loop : 0.80 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 70 HIS 0.004 0.001 HIS A 540 PHE 0.015 0.001 PHE D 49 TYR 0.016 0.002 TYR C 460 ARG 0.011 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8132 (mt0) cc_final: 0.7785 (mt0) REVERT: B 35 LEU cc_start: 0.7874 (mp) cc_final: 0.7672 (tt) REVERT: B 91 GLU cc_start: 0.8010 (pt0) cc_final: 0.7804 (pm20) REVERT: B 126 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8722 (ptpp) REVERT: B 133 LYS cc_start: 0.8710 (mppt) cc_final: 0.8333 (mmmm) REVERT: B 314 MET cc_start: 0.9071 (mtp) cc_final: 0.8665 (mtp) REVERT: B 439 CYS cc_start: 0.8685 (p) cc_final: 0.8184 (t) REVERT: C 66 ARG cc_start: 0.7398 (ttp80) cc_final: 0.7155 (ttp80) REVERT: D 91 GLU cc_start: 0.8273 (pt0) cc_final: 0.7681 (pm20) REVERT: D 126 LYS cc_start: 0.8747 (mtmp) cc_final: 0.8520 (ptpt) REVERT: D 568 THR cc_start: 0.8888 (m) cc_final: 0.8481 (p) REVERT: A 23 GLN cc_start: 0.8385 (mt0) cc_final: 0.7820 (mt0) REVERT: A 34 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: A 61 GLN cc_start: 0.8044 (mt0) cc_final: 0.7571 (mt0) outliers start: 29 outliers final: 11 residues processed: 230 average time/residue: 1.4728 time to fit residues: 384.0827 Evaluate side-chains 223 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 266 LYS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 249 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN A 68 HIS A 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21931 Z= 0.325 Angle : 0.574 10.325 29821 Z= 0.286 Chirality : 0.042 0.244 3207 Planarity : 0.005 0.051 3877 Dihedral : 6.407 150.857 2935 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 10.28 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2646 helix: 1.79 (0.15), residues: 1158 sheet: -0.50 (0.24), residues: 328 loop : 0.84 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 70 HIS 0.004 0.001 HIS A 540 PHE 0.014 0.002 PHE D 49 TYR 0.016 0.002 TYR C 460 ARG 0.012 0.001 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 213 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8182 (mt0) cc_final: 0.7782 (mt0) REVERT: B 35 LEU cc_start: 0.7828 (mp) cc_final: 0.7606 (tt) REVERT: B 126 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8697 (ptpp) REVERT: B 210 GLN cc_start: 0.8243 (mt0) cc_final: 0.7822 (pt0) REVERT: B 314 MET cc_start: 0.9049 (mtp) cc_final: 0.8644 (mtp) REVERT: B 439 CYS cc_start: 0.8673 (p) cc_final: 0.8196 (t) REVERT: C 66 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7121 (ttp80) REVERT: D 91 GLU cc_start: 0.8259 (pt0) cc_final: 0.7692 (pm20) REVERT: D 126 LYS cc_start: 0.8703 (mtmp) cc_final: 0.8477 (ptpt) REVERT: D 449 ASP cc_start: 0.8564 (t70) cc_final: 0.8362 (t0) REVERT: D 568 THR cc_start: 0.8905 (m) cc_final: 0.8490 (p) REVERT: D 621 LYS cc_start: 0.8618 (mttm) cc_final: 0.8122 (mppt) REVERT: A 23 GLN cc_start: 0.8426 (mt0) cc_final: 0.7837 (mt0) REVERT: A 34 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: A 61 GLN cc_start: 0.8073 (mt0) cc_final: 0.7609 (mt0) outliers start: 25 outliers final: 15 residues processed: 231 average time/residue: 1.4499 time to fit residues: 380.0230 Evaluate side-chains 219 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 136 GLN A 68 HIS A 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21931 Z= 0.206 Angle : 0.528 10.024 29821 Z= 0.262 Chirality : 0.040 0.230 3207 Planarity : 0.004 0.052 3877 Dihedral : 6.178 153.568 2935 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.09 % Allowed : 10.54 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2646 helix: 1.96 (0.15), residues: 1154 sheet: -0.48 (0.24), residues: 328 loop : 0.83 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 70 HIS 0.004 0.001 HIS A 540 PHE 0.013 0.001 PHE D 49 TYR 0.014 0.001 TYR A 474 ARG 0.013 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8230 (mt0) cc_final: 0.7850 (mt0) REVERT: B 35 LEU cc_start: 0.7846 (mp) cc_final: 0.7593 (tt) REVERT: B 126 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8694 (mttm) REVERT: B 314 MET cc_start: 0.8979 (mtp) cc_final: 0.8566 (mtp) REVERT: B 439 CYS cc_start: 0.8679 (p) cc_final: 0.8160 (t) REVERT: C 66 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7163 (ttp80) REVERT: D 91 GLU cc_start: 0.8186 (pt0) cc_final: 0.7692 (pm20) REVERT: D 126 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8544 (ptpt) REVERT: D 449 ASP cc_start: 0.8265 (t70) cc_final: 0.8001 (t0) REVERT: D 568 THR cc_start: 0.8894 (m) cc_final: 0.8509 (p) REVERT: D 621 LYS cc_start: 0.8612 (mttm) cc_final: 0.8058 (mppt) REVERT: A 23 GLN cc_start: 0.8408 (mt0) cc_final: 0.7862 (mt0) REVERT: A 61 GLN cc_start: 0.8093 (mt0) cc_final: 0.7624 (mt0) REVERT: A 571 ASP cc_start: 0.8833 (m-30) cc_final: 0.8570 (p0) outliers start: 24 outliers final: 11 residues processed: 231 average time/residue: 1.4471 time to fit residues: 379.4226 Evaluate side-chains 215 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 435 GLN B 625 ASN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 198 ASN C 480 HIS C 522 GLN D 539 GLN A 68 HIS A 269 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21931 Z= 0.255 Angle : 0.552 10.514 29821 Z= 0.273 Chirality : 0.041 0.223 3207 Planarity : 0.004 0.056 3877 Dihedral : 6.238 156.692 2935 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.05 % Allowed : 10.89 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2646 helix: 1.95 (0.15), residues: 1158 sheet: -0.43 (0.25), residues: 328 loop : 0.86 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 176 HIS 0.004 0.001 HIS A 540 PHE 0.013 0.001 PHE D 49 TYR 0.022 0.002 TYR A 474 ARG 0.015 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8223 (mt0) cc_final: 0.7834 (mt0) REVERT: B 35 LEU cc_start: 0.7856 (mp) cc_final: 0.7597 (tt) REVERT: B 126 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8707 (mttm) REVERT: B 133 LYS cc_start: 0.8559 (mppt) cc_final: 0.8080 (mmtp) REVERT: B 210 GLN cc_start: 0.8251 (mt0) cc_final: 0.7818 (pt0) REVERT: B 314 MET cc_start: 0.9010 (mtp) cc_final: 0.8597 (mtp) REVERT: B 439 CYS cc_start: 0.8685 (p) cc_final: 0.8168 (t) REVERT: C 66 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7130 (ttp80) REVERT: D 34 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: D 84 GLN cc_start: 0.7422 (tp40) cc_final: 0.6705 (tp-100) REVERT: D 91 GLU cc_start: 0.8149 (pt0) cc_final: 0.7875 (mp0) REVERT: D 126 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8549 (ptpt) REVERT: D 568 THR cc_start: 0.8906 (m) cc_final: 0.8513 (p) REVERT: D 621 LYS cc_start: 0.8611 (mttm) cc_final: 0.8055 (mppt) REVERT: A 5 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7618 (ttm-80) REVERT: A 23 GLN cc_start: 0.8403 (mt0) cc_final: 0.7988 (mt0) REVERT: A 34 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 61 GLN cc_start: 0.8083 (mt0) cc_final: 0.7598 (mt0) REVERT: A 571 ASP cc_start: 0.8824 (m-30) cc_final: 0.8558 (p0) outliers start: 23 outliers final: 14 residues processed: 224 average time/residue: 1.4699 time to fit residues: 373.1518 Evaluate side-chains 222 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 303 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 435 GLN B 625 ASN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN A 68 HIS A 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21931 Z= 0.310 Angle : 0.575 10.974 29821 Z= 0.285 Chirality : 0.042 0.222 3207 Planarity : 0.005 0.092 3877 Dihedral : 6.348 160.823 2935 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.96 % Allowed : 11.07 % 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: 1.62 (0.16), residues: 2646 helix: 1.91 (0.15), residues: 1158 sheet: -0.44 (0.25), residues: 328 loop : 0.86 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 176 HIS 0.004 0.001 HIS A 540 PHE 0.012 0.001 PHE D 49 TYR 0.020 0.002 TYR A 474 ARG 0.019 0.001 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8211 (mt0) cc_final: 0.7834 (mt0) REVERT: B 35 LEU cc_start: 0.7831 (mp) cc_final: 0.7574 (tt) REVERT: B 126 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8673 (ptpp) REVERT: B 210 GLN cc_start: 0.8228 (mt0) cc_final: 0.7789 (pt0) REVERT: B 314 MET cc_start: 0.9036 (mtp) cc_final: 0.8670 (mtp) REVERT: B 439 CYS cc_start: 0.8678 (p) cc_final: 0.8191 (t) REVERT: C 66 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7063 (ttp80) REVERT: D 5 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7152 (ttp80) REVERT: D 34 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: D 84 GLN cc_start: 0.6970 (tp40) cc_final: 0.6210 (tp-100) REVERT: D 91 GLU cc_start: 0.8135 (pt0) cc_final: 0.7809 (mp0) REVERT: D 126 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8549 (ptpt) REVERT: D 265 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 568 THR cc_start: 0.8916 (m) cc_final: 0.8505 (p) REVERT: D 621 LYS cc_start: 0.8619 (mttm) cc_final: 0.8060 (mppt) REVERT: D 632 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8255 (mm-30) REVERT: A 23 GLN cc_start: 0.8401 (mt0) cc_final: 0.7963 (mt0) REVERT: A 34 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 61 GLN cc_start: 0.8072 (mt0) cc_final: 0.7593 (mt0) outliers start: 21 outliers final: 14 residues processed: 226 average time/residue: 1.5323 time to fit residues: 391.8895 Evaluate side-chains 219 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.0030 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 142 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN B 625 ASN C 198 ASN D 198 ASN A 68 HIS A 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21931 Z= 0.159 Angle : 0.518 11.308 29821 Z= 0.256 Chirality : 0.039 0.208 3207 Planarity : 0.005 0.091 3877 Dihedral : 6.082 163.111 2935 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.74 % Allowed : 11.42 % Favored : 87.84 % 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: 1.71 (0.16), residues: 2646 helix: 2.09 (0.15), residues: 1130 sheet: -0.39 (0.25), residues: 328 loop : 0.82 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 70 HIS 0.003 0.001 HIS A 540 PHE 0.013 0.001 PHE D 49 TYR 0.022 0.001 TYR A 474 ARG 0.017 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7376 (ttp80) REVERT: B 23 GLN cc_start: 0.8163 (mt0) cc_final: 0.7440 (mp-120) REVERT: B 126 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8702 (mttm) REVERT: B 314 MET cc_start: 0.8932 (mtp) cc_final: 0.8521 (mtp) REVERT: B 439 CYS cc_start: 0.8695 (p) cc_final: 0.8124 (t) REVERT: B 568 THR cc_start: 0.9071 (m) cc_final: 0.8519 (p) REVERT: C 7 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8261 (mtp85) REVERT: C 66 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7131 (ttp80) REVERT: D 5 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7302 (ttp80) REVERT: D 39 LEU cc_start: 0.8483 (mt) cc_final: 0.8269 (mp) REVERT: D 265 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 568 THR cc_start: 0.8864 (m) cc_final: 0.8499 (p) REVERT: A 23 GLN cc_start: 0.8399 (mt0) cc_final: 0.7960 (mt0) REVERT: A 61 GLN cc_start: 0.8086 (mt0) cc_final: 0.7606 (mt0) REVERT: A 265 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7761 (mp0) REVERT: A 571 ASP cc_start: 0.8813 (m-30) cc_final: 0.8580 (p0) outliers start: 16 outliers final: 6 residues processed: 221 average time/residue: 1.4783 time to fit residues: 370.1158 Evaluate side-chains 205 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain A residue 249 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN B 625 ASN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 435 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 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 : 0.003 0.038 21931 Z= 0.202 Angle : 0.538 12.777 29821 Z= 0.266 Chirality : 0.040 0.203 3207 Planarity : 0.005 0.080 3877 Dihedral : 6.139 163.441 2935 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.61 % Allowed : 11.68 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2646 helix: 2.06 (0.15), residues: 1130 sheet: -0.29 (0.25), residues: 328 loop : 0.84 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 70 HIS 0.004 0.001 HIS A 540 PHE 0.012 0.001 PHE D 49 TYR 0.027 0.001 TYR A 474 ARG 0.018 0.000 ARG A 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7392 (ttp80) REVERT: B 23 GLN cc_start: 0.7999 (mt0) cc_final: 0.7496 (mp-120) REVERT: B 35 LEU cc_start: 0.7923 (mp) cc_final: 0.7608 (tt) REVERT: B 48 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7862 (mm-30) REVERT: B 126 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8716 (mttm) REVERT: B 210 GLN cc_start: 0.8239 (mt0) cc_final: 0.7827 (pt0) REVERT: B 314 MET cc_start: 0.8970 (mtp) cc_final: 0.8565 (mtp) REVERT: B 439 CYS cc_start: 0.8686 (p) cc_final: 0.8151 (t) REVERT: C 66 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7096 (ttp80) REVERT: C 265 GLU cc_start: 0.8134 (mp0) cc_final: 0.7932 (mp0) REVERT: D 5 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7200 (ttp80) REVERT: D 39 LEU cc_start: 0.8478 (mt) cc_final: 0.8265 (mp) REVERT: D 265 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8048 (mt-10) REVERT: D 568 THR cc_start: 0.8899 (m) cc_final: 0.8515 (p) REVERT: D 621 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8358 (mttm) REVERT: A 23 GLN cc_start: 0.8369 (mt0) cc_final: 0.7842 (mt0) REVERT: A 61 GLN cc_start: 0.8083 (mt0) cc_final: 0.7632 (mt0) REVERT: A 571 ASP cc_start: 0.8773 (m-30) cc_final: 0.8547 (p0) outliers start: 13 outliers final: 9 residues processed: 214 average time/residue: 1.4914 time to fit residues: 362.2619 Evaluate side-chains 212 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 193 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075208 restraints weight = 47972.585| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.56 r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21931 Z= 0.196 Angle : 0.537 9.356 29821 Z= 0.267 Chirality : 0.040 0.202 3207 Planarity : 0.005 0.086 3877 Dihedral : 6.152 166.067 2935 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.57 % Allowed : 11.72 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2646 helix: 2.05 (0.15), residues: 1130 sheet: -0.24 (0.25), residues: 328 loop : 0.84 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 70 HIS 0.004 0.001 HIS D 127 PHE 0.012 0.001 PHE D 49 TYR 0.026 0.001 TYR A 474 ARG 0.020 0.000 ARG A 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8927.00 seconds wall clock time: 158 minutes 53.33 seconds (9533.33 seconds total)