Starting phenix.real_space_refine on Sat Sep 28 17:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/09_2024/7dkj_30707.cif" } resolution = 3.7 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= 0.000 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12633 2.51 5 N 3381 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20112 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "E" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "I" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.63, per 1000 atoms: 0.58 Number of scatterers: 20112 At special positions: 0 Unit cell: (154.35, 149.94, 148.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3984 8.00 N 3381 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS D 147 " distance=1.92 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 464 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.02 Simple disulfide: pdb=" SG CYS E 471 " - pdb=" SG CYS E 475 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS H 147 " distance=1.97 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 464 " distance=2.03 Simple disulfide: pdb=" SG CYS I 44 " - pdb=" SG CYS I 275 " distance=2.03 Simple disulfide: pdb=" SG CYS I 57 " - pdb=" SG CYS I 69 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 303 " distance=2.02 Simple disulfide: pdb=" SG CYS I 471 " - pdb=" SG CYS I 475 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS L 147 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 13 " " NAG A 602 " - " ASN A 25 " " NAG A 603 " - " ASN A 287 " " NAG B 1 " - " ASN A 166 " " NAG E 601 " - " ASN E 13 " " NAG E 602 " - " ASN E 25 " " NAG E 603 " - " ASN E 287 " " NAG F 1 " - " ASN A 481 " " NAG I 601 " - " ASN I 13 " " NAG I 602 " - " ASN I 25 " " NAG I 603 " - " ASN I 287 " " NAG J 1 " - " ASN E 166 " " NAG M 1 " - " ASN E 481 " " NAG N 1 " - " ASN I 166 " " NAG O 1 " - " ASN I 481 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 45 sheets defined 28.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 133 through 170 Proline residue: C 146 - end of helix Proline residue: C 165 - end of helix Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Proline residue: D 151 - end of helix removed outlier: 3.715A pdb=" N LYS D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 364 through 386 Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 453 removed outlier: 3.939A pdb=" N LEU E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 481 Processing helix chain 'E' and resid 485 through 499 removed outlier: 3.824A pdb=" N TYR E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 491 " --> pdb=" O PRO E 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.842A pdb=" N ASN G 56 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 133 through 170 Proline residue: G 146 - end of helix Proline residue: G 165 - end of helix Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN H 124 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Proline residue: H 132 - end of helix Proline residue: H 151 - end of helix removed outlier: 3.715A pdb=" N LYS H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 99 through 108 Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'I' and resid 364 through 386 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU I 426 " --> pdb=" O ASN I 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 481 Processing helix chain 'I' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR I 489 " --> pdb=" O ASP I 485 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 491 " --> pdb=" O PRO I 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU I 492 " --> pdb=" O LYS I 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU I 499 " --> pdb=" O LEU I 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN K 56 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 133 through 170 Proline residue: K 146 - end of helix Proline residue: K 165 - end of helix Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Proline residue: L 132 - end of helix Proline residue: L 151 - end of helix removed outlier: 3.715A pdb=" N LYS L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS A 45 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.817A pdb=" N ILE A 81 " --> pdb=" O ILE A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=AA9, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.026A pdb=" N ILE C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 98 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP C 112 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG C 100 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS E 45 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.819A pdb=" N ILE E 81 " --> pdb=" O ILE E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE G 80 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS G 98 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP G 112 " --> pdb=" O CYS G 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG G 100 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AD6, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS I 45 " --> pdb=" O THR I 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.818A pdb=" N ILE I 81 " --> pdb=" O ILE I 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 176 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 161 through 165 Processing sheet with id=AE3, first strand: chain 'I' and resid 292 through 293 Processing sheet with id=AE4, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE K 80 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS K 98 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP K 112 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG K 100 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'L' and resid 53 through 54 822 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 6.38 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: 6501 1.34 - 1.46: 4648 1.46 - 1.58: 9233 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 20550 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.570 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CG1 ILE A 383 " pdb=" CD1 ILE A 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.29e+00 bond pdb=" CG1 ILE E 383 " pdb=" CD1 ILE E 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 26860 2.09 - 4.18: 780 4.18 - 6.26: 105 6.26 - 8.35: 38 8.35 - 10.44: 12 Bond angle restraints: 27795 Sorted by residual: angle pdb=" CA GLN K 78 " pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN C 78 " pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN G 78 " pdb=" CB GLN G 78 " pdb=" CG GLN G 78 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " pdb=" CD GLN C 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " pdb=" CD GLN K 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 ... (remaining 27790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 11331 21.28 - 42.56: 955 42.56 - 63.84: 172 63.84 - 85.11: 119 85.11 - 106.39: 104 Dihedral angle restraints: 12681 sinusoidal: 5529 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS E 44 " pdb=" SG CYS E 44 " pdb=" SG CYS E 275 " pdb=" CB CYS E 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.61 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS I 44 " pdb=" SG CYS I 44 " pdb=" SG CYS I 275 " pdb=" CB CYS I 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.62 -76.38 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 275 " pdb=" CB CYS A 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.64 -76.36 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 12678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2846 0.097 - 0.194: 190 0.194 - 0.291: 9 0.291 - 0.387: 0 0.387 - 0.484: 3 Chirality restraints: 3048 Sorted by residual: chirality pdb=" C1 NAG I 602 " pdb=" ND2 ASN I 25 " pdb=" C2 NAG I 602 " pdb=" O5 NAG I 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 3045 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO D 95 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 94 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO L 95 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO H 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " 0.040 5.00e-02 4.00e+02 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 348 2.62 - 3.19: 19418 3.19 - 3.76: 31253 3.76 - 4.33: 43362 4.33 - 4.90: 71032 Nonbonded interactions: 165413 Sorted by model distance: nonbonded pdb=" OG1 THR E 128 " pdb=" OG1 THR E 152 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 152 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR I 128 " pdb=" OG1 THR I 152 " model vdw 2.056 3.040 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.090 3.120 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.090 3.120 ... (remaining 165408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 44.900 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 0.098 20550 Z= 0.485 Angle : 0.873 10.440 27795 Z= 0.463 Chirality : 0.054 0.484 3048 Planarity : 0.005 0.072 3567 Dihedral : 20.249 106.392 8040 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.84 % Allowed : 2.26 % Favored : 95.90 % 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: -2.34 (0.16), residues: 2472 helix: -1.01 (0.20), residues: 597 sheet: -1.31 (0.22), residues: 567 loop : -1.91 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 150 HIS 0.005 0.001 HIS I 10 PHE 0.015 0.002 PHE I 229 TYR 0.023 0.002 TYR L 145 ARG 0.012 0.002 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 418 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 337 ILE cc_start: 0.8898 (mm) cc_final: 0.8591 (mm) REVERT: A 411 MET cc_start: 0.8349 (tmm) cc_final: 0.7653 (tmm) REVERT: A 412 GLU cc_start: 0.7140 (tt0) cc_final: 0.6598 (tt0) REVERT: A 433 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5783 (mmt-90) REVERT: A 451 MET cc_start: 0.8506 (ttm) cc_final: 0.8280 (ttm) REVERT: C 78 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.4934 (pt0) REVERT: C 96 TYR cc_start: 0.7132 (m-80) cc_final: 0.6758 (m-80) REVERT: C 109 MET cc_start: 0.8181 (mmm) cc_final: 0.7926 (mmm) REVERT: D 145 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.3807 (m-10) REVERT: E 21 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8198 (tp) REVERT: E 93 PHE cc_start: 0.7461 (t80) cc_final: 0.7185 (t80) REVERT: E 175 ILE cc_start: 0.9200 (mm) cc_final: 0.8904 (mm) REVERT: E 236 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6507 (mmp) REVERT: E 260 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7511 (mmp80) REVERT: E 271 THR cc_start: 0.8401 (t) cc_final: 0.8098 (m) REVERT: E 308 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7951 (mttm) REVERT: E 324 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6381 (pt) REVERT: E 337 ILE cc_start: 0.9031 (mm) cc_final: 0.8701 (mm) REVERT: E 341 TRP cc_start: 0.8748 (m-10) cc_final: 0.8383 (m-10) REVERT: E 411 MET cc_start: 0.8436 (tmm) cc_final: 0.7977 (tmm) REVERT: E 412 GLU cc_start: 0.7038 (tt0) cc_final: 0.6689 (mt-10) REVERT: E 468 TYR cc_start: 0.7936 (m-80) cc_final: 0.7404 (m-80) REVERT: G 12 VAL cc_start: 0.8499 (t) cc_final: 0.8078 (m) REVERT: G 31 ASP cc_start: 0.7817 (p0) cc_final: 0.7576 (p0) REVERT: G 33 TYR cc_start: 0.7753 (m-80) cc_final: 0.7549 (m-10) REVERT: G 34 MET cc_start: 0.6892 (tpp) cc_final: 0.6675 (tpt) REVERT: G 35 THR cc_start: 0.7670 (m) cc_final: 0.7402 (m) REVERT: G 71 THR cc_start: 0.7846 (p) cc_final: 0.7620 (p) REVERT: G 73 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (m) REVERT: G 78 GLN cc_start: 0.5270 (OUTLIER) cc_final: 0.4974 (mp10) REVERT: G 109 MET cc_start: 0.7563 (mmm) cc_final: 0.7233 (mmm) REVERT: H 145 TYR cc_start: 0.4181 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: I 83 GLU cc_start: 0.7409 (tt0) cc_final: 0.6882 (tt0) REVERT: I 93 PHE cc_start: 0.7395 (t80) cc_final: 0.7133 (t80) REVERT: I 146 ARG cc_start: 0.6687 (mpt180) cc_final: 0.6477 (mmt-90) REVERT: I 236 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: I 308 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8271 (mttp) REVERT: I 324 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (pt) REVERT: I 355 ASN cc_start: 0.8739 (t0) cc_final: 0.8458 (t0) REVERT: I 468 TYR cc_start: 0.8669 (m-80) cc_final: 0.8448 (m-80) REVERT: K 12 VAL cc_start: 0.7479 (t) cc_final: 0.7190 (m) REVERT: K 13 GLN cc_start: 0.7329 (mm110) cc_final: 0.7092 (mm110) REVERT: K 73 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7345 (m) REVERT: K 109 MET cc_start: 0.7504 (mmm) cc_final: 0.7156 (mmm) REVERT: K 149 GLU cc_start: 0.4278 (mp0) cc_final: 0.3895 (mm-30) REVERT: L 145 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3674 (m-80) outliers start: 40 outliers final: 7 residues processed: 444 average time/residue: 0.3226 time to fit residues: 216.8441 Evaluate side-chains 342 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 321 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 353 HIS A 477 ASN C 13 GLN C 157 GLN D 6 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 353 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN E 477 ASN G 157 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 146 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 377 ASN I 477 ASN K 157 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20550 Z= 0.227 Angle : 0.726 8.729 27795 Z= 0.370 Chirality : 0.049 0.399 3048 Planarity : 0.005 0.055 3567 Dihedral : 14.436 81.324 3304 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.12 % Allowed : 10.42 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2472 helix: 0.73 (0.22), residues: 591 sheet: -1.24 (0.22), residues: 534 loop : -1.75 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 150 HIS 0.012 0.002 HIS A 353 PHE 0.012 0.002 PHE I 372 TYR 0.022 0.002 TYR K 62 ARG 0.007 0.001 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 341 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7890 (mm) cc_final: 0.7637 (tp) REVERT: A 36 GLU cc_start: 0.7002 (tp30) cc_final: 0.6761 (tp30) REVERT: A 337 ILE cc_start: 0.8969 (mm) cc_final: 0.8573 (mm) REVERT: A 411 MET cc_start: 0.8760 (tmm) cc_final: 0.8323 (tmm) REVERT: A 412 GLU cc_start: 0.7123 (tt0) cc_final: 0.6461 (mt-10) REVERT: A 433 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6239 (mtt-85) REVERT: C 34 MET cc_start: 0.7822 (tpp) cc_final: 0.7585 (tpp) REVERT: C 60 THR cc_start: 0.8105 (m) cc_final: 0.7468 (p) REVERT: C 62 TYR cc_start: 0.7697 (m-80) cc_final: 0.6939 (m-80) REVERT: C 78 GLN cc_start: 0.6316 (mp10) cc_final: 0.5687 (pt0) REVERT: C 144 LEU cc_start: 0.4974 (tt) cc_final: 0.4479 (mp) REVERT: C 148 MET cc_start: 0.3109 (mtp) cc_final: 0.2516 (ttp) REVERT: E 271 THR cc_start: 0.8481 (t) cc_final: 0.8147 (m) REVERT: E 308 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8039 (mttm) REVERT: E 324 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6207 (pt) REVERT: E 337 ILE cc_start: 0.9038 (mm) cc_final: 0.8727 (mm) REVERT: E 341 TRP cc_start: 0.8600 (m-10) cc_final: 0.8254 (m-10) REVERT: E 353 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.6375 (p-80) REVERT: E 411 MET cc_start: 0.8757 (tmm) cc_final: 0.8478 (tmm) REVERT: E 412 GLU cc_start: 0.6884 (tt0) cc_final: 0.6601 (mt-10) REVERT: E 433 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6650 (mmp80) REVERT: E 466 GLU cc_start: 0.7980 (tt0) cc_final: 0.7682 (tt0) REVERT: E 468 TYR cc_start: 0.7887 (m-80) cc_final: 0.7539 (m-80) REVERT: G 12 VAL cc_start: 0.8434 (t) cc_final: 0.7969 (m) REVERT: G 31 ASP cc_start: 0.7693 (p0) cc_final: 0.7384 (p0) REVERT: G 70 PHE cc_start: 0.7481 (m-10) cc_final: 0.7263 (m-10) REVERT: G 109 MET cc_start: 0.7690 (mmm) cc_final: 0.7473 (mmm) REVERT: G 149 GLU cc_start: 0.2152 (mp0) cc_final: 0.1771 (mm-30) REVERT: H 133 MET cc_start: 0.1603 (ppp) cc_final: 0.0607 (tpt) REVERT: I 83 GLU cc_start: 0.7381 (tt0) cc_final: 0.6946 (tt0) REVERT: I 115 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7825 (ttmm) REVERT: I 217 ARG cc_start: 0.7151 (mtt90) cc_final: 0.6776 (mtt90) REVERT: I 308 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8268 (mttp) REVERT: I 324 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7464 (pt) REVERT: I 337 ILE cc_start: 0.9183 (mm) cc_final: 0.8785 (mm) REVERT: I 355 ASN cc_start: 0.8496 (t0) cc_final: 0.8221 (t0) REVERT: I 433 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6191 (mmp-170) REVERT: K 12 VAL cc_start: 0.7486 (t) cc_final: 0.7258 (m) REVERT: K 31 ASP cc_start: 0.7440 (p0) cc_final: 0.7074 (p0) REVERT: K 74 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7510 (ptp90) REVERT: K 78 GLN cc_start: 0.5039 (mp10) cc_final: 0.4763 (pt0) REVERT: K 110 ASP cc_start: 0.8388 (p0) cc_final: 0.8093 (p0) REVERT: L 134 MET cc_start: 0.2140 (mtp) cc_final: 0.1110 (mtp) outliers start: 46 outliers final: 25 residues processed: 364 average time/residue: 0.3344 time to fit residues: 184.5265 Evaluate side-chains 339 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 308 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 238 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 377 ASN E 469 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20550 Z= 0.259 Angle : 0.671 8.132 27795 Z= 0.340 Chirality : 0.048 0.387 3048 Planarity : 0.005 0.058 3567 Dihedral : 10.956 69.797 3277 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.90 % Allowed : 12.96 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2472 helix: 1.11 (0.22), residues: 591 sheet: -1.16 (0.22), residues: 528 loop : -1.74 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 150 HIS 0.015 0.001 HIS E 353 PHE 0.012 0.002 PHE I 372 TYR 0.022 0.002 TYR K 82 ARG 0.006 0.001 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 333 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.6760 (mtm180) REVERT: A 56 ASP cc_start: 0.5463 (t0) cc_final: 0.5139 (t0) REVERT: A 337 ILE cc_start: 0.9124 (mm) cc_final: 0.8808 (mm) REVERT: A 411 MET cc_start: 0.9061 (tmm) cc_final: 0.8523 (tmm) REVERT: A 433 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6385 (mtt-85) REVERT: C 31 ASP cc_start: 0.7560 (p0) cc_final: 0.7350 (p0) REVERT: C 60 THR cc_start: 0.8203 (m) cc_final: 0.7675 (p) REVERT: C 62 TYR cc_start: 0.7785 (m-80) cc_final: 0.6953 (m-80) REVERT: C 78 GLN cc_start: 0.6151 (mp10) cc_final: 0.5741 (pt0) REVERT: C 144 LEU cc_start: 0.5182 (tt) cc_final: 0.4840 (mp) REVERT: D 74 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6786 (mmtt) REVERT: E 115 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7136 (ttmt) REVERT: E 271 THR cc_start: 0.8486 (t) cc_final: 0.8177 (m) REVERT: E 308 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8399 (mttt) REVERT: E 324 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6519 (pt) REVERT: E 337 ILE cc_start: 0.9108 (mm) cc_final: 0.8846 (mm) REVERT: E 411 MET cc_start: 0.8836 (tmm) cc_final: 0.8489 (tmm) REVERT: E 412 GLU cc_start: 0.6994 (tt0) cc_final: 0.6788 (mt-10) REVERT: E 433 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6489 (tpt-90) REVERT: E 466 GLU cc_start: 0.7917 (tt0) cc_final: 0.7571 (tt0) REVERT: E 468 TYR cc_start: 0.7913 (m-80) cc_final: 0.7517 (m-80) REVERT: G 12 VAL cc_start: 0.8295 (t) cc_final: 0.7941 (m) REVERT: G 75 ASP cc_start: 0.5877 (p0) cc_final: 0.4963 (p0) REVERT: G 82 TYR cc_start: 0.5536 (m-80) cc_final: 0.4987 (m-80) REVERT: G 149 GLU cc_start: 0.3232 (mp0) cc_final: 0.2550 (mm-30) REVERT: I 83 GLU cc_start: 0.7463 (tt0) cc_final: 0.7017 (tt0) REVERT: I 115 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7822 (ttmm) REVERT: I 217 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6782 (mtt90) REVERT: I 308 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8290 (mttp) REVERT: I 324 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7294 (pt) REVERT: I 355 ASN cc_start: 0.8523 (t0) cc_final: 0.8070 (t0) REVERT: I 433 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6529 (tpt-90) REVERT: I 466 GLU cc_start: 0.7708 (tt0) cc_final: 0.7399 (tm-30) REVERT: I 486 TYR cc_start: 0.8134 (t80) cc_final: 0.7865 (t80) REVERT: K 31 ASP cc_start: 0.7537 (p0) cc_final: 0.7156 (p0) REVERT: K 74 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7439 (ptm160) REVERT: K 149 GLU cc_start: 0.4036 (mm-30) cc_final: 0.3829 (mm-30) REVERT: L 74 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7058 (mtmt) outliers start: 63 outliers final: 35 residues processed: 370 average time/residue: 0.3158 time to fit residues: 178.1814 Evaluate side-chains 331 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 290 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 79 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 408 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20550 Z= 0.369 Angle : 0.717 9.702 27795 Z= 0.367 Chirality : 0.049 0.413 3048 Planarity : 0.005 0.060 3567 Dihedral : 9.469 59.217 3277 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.23 % Allowed : 16.92 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2472 helix: 0.94 (0.21), residues: 594 sheet: -1.31 (0.22), residues: 534 loop : -1.73 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 150 HIS 0.013 0.002 HIS E 353 PHE 0.016 0.002 PHE I 372 TYR 0.027 0.002 TYR C 82 ARG 0.005 0.001 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 317 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.6904 (mtm180) REVERT: A 337 ILE cc_start: 0.9060 (mm) cc_final: 0.8664 (mm) REVERT: A 349 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: A 411 MET cc_start: 0.8861 (tmm) cc_final: 0.8298 (tmm) REVERT: A 433 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6446 (mtt-85) REVERT: C 74 ARG cc_start: 0.6941 (ptp90) cc_final: 0.6667 (ptp90) REVERT: C 78 GLN cc_start: 0.5823 (mp10) cc_final: 0.5606 (pt0) REVERT: C 144 LEU cc_start: 0.5261 (tt) cc_final: 0.4867 (mp) REVERT: D 6 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.5709 (mm110) REVERT: E 146 ARG cc_start: 0.7628 (mmt-90) cc_final: 0.7117 (mmt-90) REVERT: E 302 GLU cc_start: 0.6728 (tt0) cc_final: 0.5019 (tp30) REVERT: E 308 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8340 (mttt) REVERT: E 337 ILE cc_start: 0.9186 (mm) cc_final: 0.8810 (mm) REVERT: E 411 MET cc_start: 0.8741 (tmm) cc_final: 0.8528 (tmm) REVERT: E 433 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6224 (tpt170) REVERT: E 466 GLU cc_start: 0.7934 (tt0) cc_final: 0.7657 (tt0) REVERT: E 468 TYR cc_start: 0.8007 (m-80) cc_final: 0.7490 (m-80) REVERT: G 12 VAL cc_start: 0.8294 (t) cc_final: 0.7949 (m) REVERT: G 107 TYR cc_start: 0.8640 (m-10) cc_final: 0.8367 (m-10) REVERT: G 149 GLU cc_start: 0.2730 (mp0) cc_final: 0.1778 (mm-30) REVERT: I 83 GLU cc_start: 0.7234 (tt0) cc_final: 0.6838 (tt0) REVERT: I 298 LEU cc_start: 0.8778 (mt) cc_final: 0.8514 (mp) REVERT: I 308 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8367 (mttp) REVERT: I 324 ILE cc_start: 0.7693 (mt) cc_final: 0.7258 (pt) REVERT: I 337 ILE cc_start: 0.9048 (mm) cc_final: 0.8748 (mm) REVERT: I 355 ASN cc_start: 0.8825 (t0) cc_final: 0.8510 (t0) REVERT: I 429 MET cc_start: 0.7764 (mtt) cc_final: 0.7551 (mtt) REVERT: I 433 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6765 (tpt170) REVERT: K 31 ASP cc_start: 0.7515 (p0) cc_final: 0.7124 (p0) REVERT: L 74 LYS cc_start: 0.7570 (mtmm) cc_final: 0.6882 (mtmt) outliers start: 70 outliers final: 49 residues processed: 363 average time/residue: 0.3114 time to fit residues: 173.3188 Evaluate side-chains 343 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20550 Z= 0.265 Angle : 0.656 9.757 27795 Z= 0.334 Chirality : 0.046 0.405 3048 Planarity : 0.005 0.062 3567 Dihedral : 8.573 53.282 3273 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.18 % Allowed : 18.58 % Favored : 78.24 % 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: -1.36 (0.17), residues: 2472 helix: 1.07 (0.21), residues: 594 sheet: -1.33 (0.22), residues: 540 loop : -1.67 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 150 HIS 0.011 0.001 HIS E 353 PHE 0.015 0.002 PHE K 50 TYR 0.023 0.002 TYR C 82 ARG 0.005 0.000 ARG I 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 314 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.6838 (mtm-85) REVERT: A 337 ILE cc_start: 0.9044 (mm) cc_final: 0.8695 (mm) REVERT: A 349 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 411 MET cc_start: 0.8909 (tmm) cc_final: 0.8096 (tmm) REVERT: A 433 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6998 (mmp80) REVERT: A 476 MET cc_start: 0.7538 (mtp) cc_final: 0.7336 (ttm) REVERT: C 31 ASP cc_start: 0.8018 (p0) cc_final: 0.7603 (p0) REVERT: C 60 THR cc_start: 0.8567 (m) cc_final: 0.8230 (p) REVERT: C 144 LEU cc_start: 0.5218 (tt) cc_final: 0.4861 (mp) REVERT: D 74 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6792 (mmtt) REVERT: D 139 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.3905 (tp30) REVERT: E 115 LYS cc_start: 0.7427 (ttmt) cc_final: 0.6932 (ttmt) REVERT: E 146 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.6939 (mmt-90) REVERT: E 213 GLU cc_start: 0.7733 (pm20) cc_final: 0.6884 (pm20) REVERT: E 308 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8325 (mttt) REVERT: E 337 ILE cc_start: 0.9143 (mm) cc_final: 0.8845 (mm) REVERT: E 425 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8785 (tp) REVERT: E 429 MET cc_start: 0.7584 (mtp) cc_final: 0.7265 (mtt) REVERT: E 433 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.5706 (mmt90) REVERT: E 468 TYR cc_start: 0.8036 (m-80) cc_final: 0.7499 (m-80) REVERT: G 12 VAL cc_start: 0.8121 (t) cc_final: 0.7759 (m) REVERT: G 149 GLU cc_start: 0.2946 (mp0) cc_final: 0.1995 (mm-30) REVERT: I 83 GLU cc_start: 0.7353 (tt0) cc_final: 0.6901 (tt0) REVERT: I 213 GLU cc_start: 0.8284 (pm20) cc_final: 0.7719 (pm20) REVERT: I 298 LEU cc_start: 0.8756 (mt) cc_final: 0.8462 (mp) REVERT: I 308 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8334 (mttp) REVERT: I 324 ILE cc_start: 0.7691 (mt) cc_final: 0.7279 (pt) REVERT: I 337 ILE cc_start: 0.9046 (mm) cc_final: 0.8742 (mm) REVERT: I 355 ASN cc_start: 0.8595 (t0) cc_final: 0.8260 (t0) REVERT: I 433 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6789 (tpt170) REVERT: I 486 TYR cc_start: 0.8293 (t80) cc_final: 0.7745 (t80) REVERT: K 31 ASP cc_start: 0.7496 (p0) cc_final: 0.7102 (p0) REVERT: L 74 LYS cc_start: 0.7622 (mtmm) cc_final: 0.6958 (mtmt) outliers start: 69 outliers final: 51 residues processed: 361 average time/residue: 0.3056 time to fit residues: 170.6714 Evaluate side-chains 355 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 297 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 79 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 20550 Z= 0.509 Angle : 0.792 11.072 27795 Z= 0.404 Chirality : 0.051 0.435 3048 Planarity : 0.005 0.062 3567 Dihedral : 8.670 55.005 3271 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.24 % Allowed : 18.76 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % 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: -1.67 (0.16), residues: 2472 helix: 0.75 (0.21), residues: 594 sheet: -1.47 (0.22), residues: 540 loop : -1.85 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 150 HIS 0.018 0.002 HIS I 353 PHE 0.020 0.003 PHE I 415 TYR 0.024 0.002 TYR E 9 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 308 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.6886 (mtm180) REVERT: A 36 GLU cc_start: 0.7545 (tp30) cc_final: 0.7259 (tp30) REVERT: A 337 ILE cc_start: 0.9041 (mm) cc_final: 0.8657 (mm) REVERT: A 349 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: A 433 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6664 (mtt-85) REVERT: C 34 MET cc_start: 0.8400 (tpp) cc_final: 0.7741 (tpp) REVERT: C 60 THR cc_start: 0.8916 (m) cc_final: 0.8508 (p) REVERT: C 144 LEU cc_start: 0.5173 (tt) cc_final: 0.4874 (mp) REVERT: D 69 THR cc_start: 0.7078 (p) cc_final: 0.6727 (p) REVERT: D 139 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.3688 (tp30) REVERT: E 115 LYS cc_start: 0.7322 (ttmt) cc_final: 0.6609 (ttmt) REVERT: E 146 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.7033 (mmt-90) REVERT: E 308 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8314 (mttm) REVERT: E 337 ILE cc_start: 0.9151 (mm) cc_final: 0.8892 (mm) REVERT: E 349 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: E 425 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8842 (tp) REVERT: E 433 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6175 (tpt-90) REVERT: E 468 TYR cc_start: 0.8217 (m-80) cc_final: 0.7615 (m-80) REVERT: E 476 MET cc_start: 0.7594 (mtm) cc_final: 0.7393 (mtm) REVERT: G 12 VAL cc_start: 0.8350 (t) cc_final: 0.8057 (m) REVERT: G 149 GLU cc_start: 0.2340 (mp0) cc_final: 0.1535 (mm-30) REVERT: I 53 GLU cc_start: 0.7327 (tp30) cc_final: 0.6928 (tp30) REVERT: I 83 GLU cc_start: 0.7564 (tt0) cc_final: 0.7158 (tt0) REVERT: I 337 ILE cc_start: 0.9134 (mm) cc_final: 0.8802 (mm) REVERT: I 353 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.7101 (p-80) REVERT: I 355 ASN cc_start: 0.8500 (t0) cc_final: 0.8181 (t0) REVERT: I 432 GLU cc_start: 0.7661 (tp30) cc_final: 0.7125 (tp30) REVERT: I 433 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6785 (tpt170) REVERT: K 31 ASP cc_start: 0.7545 (p0) cc_final: 0.7152 (p0) REVERT: L 74 LYS cc_start: 0.7206 (mtmm) cc_final: 0.6426 (mtmt) REVERT: L 91 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: L 134 MET cc_start: 0.2929 (mtp) cc_final: 0.2401 (mtp) outliers start: 92 outliers final: 64 residues processed: 367 average time/residue: 0.3015 time to fit residues: 171.6787 Evaluate side-chains 361 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 288 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 146 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 108 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 53 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS L 53 ASN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 20550 Z= 0.391 Angle : 0.729 13.390 27795 Z= 0.372 Chirality : 0.048 0.429 3048 Planarity : 0.005 0.062 3567 Dihedral : 8.214 55.835 3267 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.20 % Allowed : 20.24 % Favored : 75.56 % 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: -1.64 (0.16), residues: 2472 helix: 0.80 (0.21), residues: 600 sheet: -1.48 (0.22), residues: 540 loop : -1.85 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 150 HIS 0.010 0.001 HIS E 353 PHE 0.016 0.002 PHE I 372 TYR 0.020 0.002 TYR E 9 ARG 0.005 0.001 ARG G 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 309 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.6869 (mtm180) REVERT: A 63 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 337 ILE cc_start: 0.9036 (mm) cc_final: 0.8640 (mm) REVERT: A 349 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: A 411 MET cc_start: 0.8749 (tmm) cc_final: 0.8318 (tmm) REVERT: A 433 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6995 (mtt-85) REVERT: C 60 THR cc_start: 0.8919 (m) cc_final: 0.8516 (p) REVERT: C 144 LEU cc_start: 0.5146 (tt) cc_final: 0.4875 (mp) REVERT: D 69 THR cc_start: 0.7030 (p) cc_final: 0.6726 (p) REVERT: D 139 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.3927 (tp30) REVERT: E 146 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.6948 (mmt-90) REVERT: E 247 ASN cc_start: 0.8652 (m110) cc_final: 0.8186 (m-40) REVERT: E 265 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8847 (mt) REVERT: E 308 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8300 (mttm) REVERT: E 337 ILE cc_start: 0.9128 (mm) cc_final: 0.8902 (mm) REVERT: E 349 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: E 425 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8775 (tp) REVERT: E 433 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6105 (tpt-90) REVERT: E 468 TYR cc_start: 0.8158 (m-80) cc_final: 0.7546 (m-80) REVERT: G 12 VAL cc_start: 0.8320 (t) cc_final: 0.8050 (m) REVERT: G 149 GLU cc_start: 0.2518 (mp0) cc_final: 0.1772 (mm-30) REVERT: H 70 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7643 (tp40) REVERT: I 53 GLU cc_start: 0.7322 (tp30) cc_final: 0.6862 (tp30) REVERT: I 83 GLU cc_start: 0.7581 (tt0) cc_final: 0.7139 (tt0) REVERT: I 337 ILE cc_start: 0.9124 (mm) cc_final: 0.8822 (mm) REVERT: I 355 ASN cc_start: 0.8522 (t0) cc_final: 0.8168 (t0) REVERT: I 432 GLU cc_start: 0.7632 (tp30) cc_final: 0.7099 (tp30) REVERT: I 433 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6843 (tpt-90) REVERT: K 31 ASP cc_start: 0.7509 (p0) cc_final: 0.7053 (p0) REVERT: L 74 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6167 (mtmt) outliers start: 91 outliers final: 71 residues processed: 372 average time/residue: 0.3025 time to fit residues: 174.1805 Evaluate side-chains 373 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 293 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS K 78 GLN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20550 Z= 0.225 Angle : 0.655 10.654 27795 Z= 0.334 Chirality : 0.046 0.406 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.496 42.505 3267 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.18 % Allowed : 21.35 % Favored : 75.47 % 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 (0.17), residues: 2472 helix: 1.09 (0.21), residues: 600 sheet: -1.42 (0.22), residues: 540 loop : -1.70 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 150 HIS 0.011 0.001 HIS I 352 PHE 0.013 0.002 PHE I 372 TYR 0.023 0.002 TYR I 253 ARG 0.010 0.001 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 323 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.6832 (mtm-85) REVERT: A 337 ILE cc_start: 0.9019 (mm) cc_final: 0.8650 (mm) REVERT: A 349 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: A 353 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6773 (p-80) REVERT: A 411 MET cc_start: 0.8698 (tmm) cc_final: 0.8272 (tmm) REVERT: A 429 MET cc_start: 0.6986 (mtp) cc_final: 0.6420 (mtt) REVERT: C 56 ASN cc_start: 0.7394 (p0) cc_final: 0.7068 (p0) REVERT: C 60 THR cc_start: 0.8793 (m) cc_final: 0.8412 (p) REVERT: C 144 LEU cc_start: 0.5116 (tt) cc_final: 0.4879 (mp) REVERT: D 69 THR cc_start: 0.6892 (p) cc_final: 0.6613 (p) REVERT: D 139 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.4050 (tp30) REVERT: E 146 ARG cc_start: 0.7112 (mmt-90) cc_final: 0.6911 (mmt-90) REVERT: E 247 ASN cc_start: 0.8523 (m110) cc_final: 0.8116 (m-40) REVERT: E 308 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8346 (mttt) REVERT: E 337 ILE cc_start: 0.9088 (mm) cc_final: 0.8856 (mm) REVERT: E 349 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: E 366 GLU cc_start: 0.6705 (tt0) cc_final: 0.6457 (tt0) REVERT: E 433 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5922 (tpt-90) REVERT: E 468 TYR cc_start: 0.8102 (m-80) cc_final: 0.7499 (m-80) REVERT: G 12 VAL cc_start: 0.8263 (t) cc_final: 0.8003 (m) REVERT: G 149 GLU cc_start: 0.3009 (mp0) cc_final: 0.1950 (mm-30) REVERT: I 83 GLU cc_start: 0.7501 (tt0) cc_final: 0.7007 (tt0) REVERT: I 337 ILE cc_start: 0.9087 (mm) cc_final: 0.8766 (mm) REVERT: I 355 ASN cc_start: 0.8548 (t0) cc_final: 0.8175 (t0) REVERT: I 432 GLU cc_start: 0.7433 (tp30) cc_final: 0.6961 (tp30) REVERT: K 31 ASP cc_start: 0.7518 (p0) cc_final: 0.6902 (p0) REVERT: K 144 LEU cc_start: 0.5506 (mp) cc_final: 0.5067 (tt) REVERT: L 74 LYS cc_start: 0.6785 (mtmm) cc_final: 0.6036 (mtmt) outliers start: 69 outliers final: 51 residues processed: 365 average time/residue: 0.3315 time to fit residues: 185.7177 Evaluate side-chains 354 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 298 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 40.0000 chunk 204 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20550 Z= 0.403 Angle : 0.731 8.657 27795 Z= 0.374 Chirality : 0.049 0.424 3048 Planarity : 0.005 0.061 3567 Dihedral : 7.542 45.605 3259 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.55 % Allowed : 20.98 % Favored : 75.47 % 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: -1.52 (0.17), residues: 2472 helix: 0.95 (0.21), residues: 600 sheet: -1.43 (0.22), residues: 540 loop : -1.78 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 150 HIS 0.012 0.002 HIS I 352 PHE 0.017 0.002 PHE I 372 TYR 0.027 0.002 TYR G 82 ARG 0.007 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.6855 (mtm180) REVERT: A 63 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 337 ILE cc_start: 0.9037 (mm) cc_final: 0.8651 (mm) REVERT: A 349 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: C 56 ASN cc_start: 0.7250 (p0) cc_final: 0.6920 (p0) REVERT: C 60 THR cc_start: 0.8893 (m) cc_final: 0.8428 (p) REVERT: C 144 LEU cc_start: 0.5085 (tt) cc_final: 0.4852 (mp) REVERT: D 69 THR cc_start: 0.7017 (p) cc_final: 0.6671 (p) REVERT: D 139 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4048 (tp30) REVERT: E 146 ARG cc_start: 0.6912 (mmt-90) cc_final: 0.6683 (mmt-90) REVERT: E 247 ASN cc_start: 0.8792 (m110) cc_final: 0.8356 (m-40) REVERT: E 308 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8294 (mttm) REVERT: E 337 ILE cc_start: 0.9101 (mm) cc_final: 0.8877 (mm) REVERT: E 349 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: E 366 GLU cc_start: 0.6873 (tt0) cc_final: 0.6645 (tt0) REVERT: E 425 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8672 (tp) REVERT: E 433 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6433 (mmm160) REVERT: E 468 TYR cc_start: 0.8243 (m-80) cc_final: 0.7413 (m-80) REVERT: G 12 VAL cc_start: 0.8250 (t) cc_final: 0.8004 (m) REVERT: G 149 GLU cc_start: 0.3013 (mp0) cc_final: 0.1963 (mm-30) REVERT: I 53 GLU cc_start: 0.7466 (tp30) cc_final: 0.7087 (tp30) REVERT: I 82 MET cc_start: 0.7737 (ptp) cc_final: 0.7433 (ptp) REVERT: I 83 GLU cc_start: 0.7567 (tt0) cc_final: 0.7151 (tt0) REVERT: I 337 ILE cc_start: 0.9125 (mm) cc_final: 0.8846 (mm) REVERT: I 355 ASN cc_start: 0.8530 (t0) cc_final: 0.8134 (t0) REVERT: I 432 GLU cc_start: 0.7647 (tp30) cc_final: 0.7151 (tp30) REVERT: K 31 ASP cc_start: 0.7591 (p0) cc_final: 0.7131 (p0) REVERT: K 144 LEU cc_start: 0.5200 (mp) cc_final: 0.4792 (tt) REVERT: L 74 LYS cc_start: 0.6846 (mtmm) cc_final: 0.6150 (mtmt) outliers start: 77 outliers final: 59 residues processed: 355 average time/residue: 0.3044 time to fit residues: 167.5856 Evaluate side-chains 356 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 291 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 192 optimal weight: 0.0020 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20550 Z= 0.224 Angle : 0.657 8.363 27795 Z= 0.337 Chirality : 0.046 0.404 3048 Planarity : 0.005 0.063 3567 Dihedral : 7.008 47.915 3259 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.72 % Allowed : 21.72 % Favored : 75.56 % 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: -1.33 (0.17), residues: 2472 helix: 1.22 (0.21), residues: 594 sheet: -1.41 (0.22), residues: 540 loop : -1.66 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 150 HIS 0.012 0.001 HIS I 352 PHE 0.017 0.002 PHE G 70 TYR 0.025 0.002 TYR G 82 ARG 0.006 0.001 ARG E 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 312 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.6834 (mtm-85) REVERT: A 63 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8216 (mm) REVERT: A 337 ILE cc_start: 0.9037 (mm) cc_final: 0.8647 (mm) REVERT: A 349 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: A 366 GLU cc_start: 0.6955 (tt0) cc_final: 0.6662 (tt0) REVERT: A 411 MET cc_start: 0.8693 (tmm) cc_final: 0.8270 (tmm) REVERT: A 429 MET cc_start: 0.6781 (mtp) cc_final: 0.6474 (mtt) REVERT: C 60 THR cc_start: 0.8801 (m) cc_final: 0.8356 (p) REVERT: C 109 MET cc_start: 0.7871 (mmm) cc_final: 0.7627 (mmm) REVERT: D 69 THR cc_start: 0.6880 (p) cc_final: 0.6659 (p) REVERT: D 139 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.4053 (tp30) REVERT: E 247 ASN cc_start: 0.8663 (m110) cc_final: 0.8299 (m-40) REVERT: E 265 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8715 (mt) REVERT: E 308 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8367 (mttt) REVERT: E 337 ILE cc_start: 0.9184 (mm) cc_final: 0.8919 (mm) REVERT: E 366 GLU cc_start: 0.6697 (tt0) cc_final: 0.6497 (tt0) REVERT: E 425 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8676 (tp) REVERT: E 433 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6881 (mmm160) REVERT: E 468 TYR cc_start: 0.8283 (m-80) cc_final: 0.7459 (m-80) REVERT: G 12 VAL cc_start: 0.8259 (t) cc_final: 0.7924 (m) REVERT: G 149 GLU cc_start: 0.3011 (mp0) cc_final: 0.1958 (mm-30) REVERT: I 83 GLU cc_start: 0.7504 (tt0) cc_final: 0.7003 (tt0) REVERT: I 337 ILE cc_start: 0.9095 (mm) cc_final: 0.8797 (mm) REVERT: I 355 ASN cc_start: 0.8545 (t0) cc_final: 0.8127 (t0) REVERT: I 432 GLU cc_start: 0.7563 (tp30) cc_final: 0.7090 (tp30) REVERT: K 31 ASP cc_start: 0.7579 (p0) cc_final: 0.6917 (p0) REVERT: K 110 ASP cc_start: 0.8484 (p0) cc_final: 0.8262 (p0) REVERT: K 144 LEU cc_start: 0.5440 (mp) cc_final: 0.5092 (tt) REVERT: L 74 LYS cc_start: 0.6790 (mtmm) cc_final: 0.6117 (mtmt) outliers start: 59 outliers final: 49 residues processed: 347 average time/residue: 0.3170 time to fit residues: 169.4560 Evaluate side-chains 358 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 303 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 177 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.174296 restraints weight = 24914.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.172087 restraints weight = 37570.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.171369 restraints weight = 48341.444| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20550 Z= 0.230 Angle : 0.657 10.230 27795 Z= 0.335 Chirality : 0.046 0.397 3048 Planarity : 0.004 0.062 3567 Dihedral : 6.671 44.029 3259 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.00 % Allowed : 21.44 % Favored : 75.56 % 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: -1.23 (0.17), residues: 2472 helix: 1.30 (0.21), residues: 600 sheet: -1.28 (0.22), residues: 531 loop : -1.64 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 150 HIS 0.010 0.001 HIS E 353 PHE 0.014 0.001 PHE I 372 TYR 0.028 0.002 TYR I 253 ARG 0.007 0.001 ARG G 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.33 seconds wall clock time: 75 minutes 22.59 seconds (4522.59 seconds total)