Starting phenix.real_space_refine on Thu Mar 5 00:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xsk_22302/03_2026/6xsk_22302.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.021 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 81 5.16 5 C 10866 2.51 5 N 2907 2.21 5 O 3468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17322 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "E" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.85, per 1000 atoms: 0.22 Number of scatterers: 17322 At special positions: 0 Unit cell: (125.19, 121.98, 151.94, 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 81 16.00 O 3468 8.00 N 2907 7.00 C 10866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS F 47 " distance=2.01 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.00 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 52 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 52 " distance=2.03 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 21 " " NAG A 403 " - " ASN A 129 " " NAG A 404 " - " ASN A 289 " " NAG B 501 " - " ASN B 154 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 129 " " NAG C 404 " - " ASN C 289 " " NAG D 501 " - " ASN D 154 " " NAG E 401 " - " ASN E 33 " " NAG E 402 " - " ASN E 21 " " NAG E 403 " - " ASN E 289 " " NAG E 404 " - " ASN E 129 " " NAG F 501 " - " ASN F 154 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN A 163 " " NAG O 1 " - " ASN A 63 " " NAG P 1 " - " ASN C 163 " " NAG Q 1 " - " ASN C 95 " " NAG R 1 " - " ASN C 63 " " NAG S 1 " - " ASN E 63 " " NAG T 1 " - " ASN E 95 " " NAG U 1 " - " ASN E 163 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 572.8 milliseconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 51 sheets defined 20.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.923A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.650A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 75 through 82 removed outlier: 4.208A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 81 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 82 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 4.265A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.632A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.669A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 74 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'J' and resid 79 through 84 removed outlier: 4.470A pdb=" N ALA J 84 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.733A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 84 removed outlier: 4.289A pdb=" N ALA K 84 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.587A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.548A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.519A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 95 " --> pdb=" O CYS H 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS H 33 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.870A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 12 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.088A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.612A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.612A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 235 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.675A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.743A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 168 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 243 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 202 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 204 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.591A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.620A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 12 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.724A pdb=" N VAL C 26 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN C 33 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.517A pdb=" N GLN C 295 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 9.126A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.831A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 268 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.709A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.709A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 235 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.707A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.918A pdb=" N ALA C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD2, first strand: chain 'F' and resid 32 through 33 removed outlier: 3.925A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 12 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.550A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.573A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.462A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 115 through 122 removed outlier: 4.742A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 115 through 122 removed outlier: 4.742A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 229 " --> pdb=" O HIS E 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.575A pdb=" N SER E 146 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER E 138 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLU E 144 " --> pdb=" O SER E 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.923A pdb=" N ALA E 247 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 166 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.675A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.754A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.535A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN J 37 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.981A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.909A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF3, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.565A pdb=" N THR K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR K 49 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.589A pdb=" N GLN I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP I 72 " --> pdb=" O GLN I 77 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 56 through 59 removed outlier: 5.417A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS I 33 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN I 39 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 98 through 99 662 hydrogen bonds defined for protein. 1788 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: 2.83 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4261 1.33 - 1.45: 3923 1.45 - 1.58: 9426 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 17712 Sorted by residual: bond pdb=" N ILE I 97 " pdb=" CA ILE I 97 " ideal model delta sigma weight residual 1.458 1.501 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" N VAL E 36 " pdb=" CA VAL E 36 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N GLN L 89 " pdb=" CA GLN L 89 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N VAL C 34 " pdb=" CA VAL C 34 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.11e-02 8.12e+03 1.10e+01 bond pdb=" N ILE I 99 " pdb=" CA ILE I 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 ... (remaining 17707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 22925 2.48 - 4.95: 1018 4.95 - 7.43: 74 7.43 - 9.90: 8 9.90 - 12.38: 5 Bond angle restraints: 24030 Sorted by residual: angle pdb=" C SER E 126 " pdb=" N TRP E 127 " pdb=" CA TRP E 127 " ideal model delta sigma weight residual 123.46 115.19 8.27 1.35e+00 5.49e-01 3.75e+01 angle pdb=" CA VAL C 29 " pdb=" C VAL C 29 " pdb=" O VAL C 29 " ideal model delta sigma weight residual 121.28 114.68 6.60 1.17e+00 7.31e-01 3.18e+01 angle pdb=" C LYS D 127 " pdb=" CA LYS D 127 " pdb=" CB LYS D 127 " ideal model delta sigma weight residual 116.63 110.72 5.91 1.16e+00 7.43e-01 2.59e+01 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 120.82 128.43 -7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C LEU F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta sigma weight residual 120.82 128.35 -7.53 1.50e+00 4.44e-01 2.52e+01 ... (remaining 24025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 10330 21.75 - 43.49: 595 43.49 - 65.24: 76 65.24 - 86.99: 35 86.99 - 108.73: 13 Dihedral angle restraints: 11049 sinusoidal: 4836 harmonic: 6213 Sorted by residual: dihedral pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -174.35 88.35 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 14.18 78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -154.11 68.11 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2083 0.074 - 0.148: 496 0.148 - 0.222: 109 0.222 - 0.296: 26 0.296 - 0.370: 7 Chirality restraints: 2721 Sorted by residual: chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 154 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA VAL A 88 " pdb=" N VAL A 88 " pdb=" C VAL A 88 " pdb=" CB VAL A 88 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA LEU L 33 " pdb=" N LEU L 33 " pdb=" C LEU L 33 " pdb=" CB LEU L 33 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2718 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 401 " -0.254 2.00e-02 2.50e+03 2.16e-01 5.82e+02 pdb=" C7 NAG E 401 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 401 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG E 401 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG E 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 404 " 0.228 2.00e-02 2.50e+03 1.90e-01 4.50e+02 pdb=" C7 NAG E 404 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 404 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG E 404 " -0.312 2.00e-02 2.50e+03 pdb=" O7 NAG E 404 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 501 " 0.182 2.00e-02 2.50e+03 1.50e-01 2.83e+02 pdb=" C7 NAG F 501 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG F 501 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG F 501 " -0.244 2.00e-02 2.50e+03 pdb=" O7 NAG F 501 " -0.020 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4005 2.80 - 3.32: 15286 3.32 - 3.85: 28707 3.85 - 4.37: 32316 4.37 - 4.90: 55228 Nonbonded interactions: 135542 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 131 " pdb=" OG1 THR A 155 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.355 3.040 nonbonded pdb=" OG SER A 39 " pdb=" NH2 ARG A 315 " model vdw 2.360 3.120 nonbonded pdb=" OE1 GLU A 175 " pdb=" NH2 ARG A 262 " model vdw 2.366 3.120 ... (remaining 135537 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' } 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: 2.920 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17777 Z= 0.436 Angle : 1.153 44.014 24196 Z= 0.719 Chirality : 0.070 0.370 2721 Planarity : 0.008 0.216 3063 Dihedral : 13.846 108.732 6990 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.37 % Allowed : 2.77 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2139 helix: 1.53 (0.27), residues: 372 sheet: 1.30 (0.24), residues: 471 loop : -0.79 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 106 TYR 0.046 0.002 TYR J 49 PHE 0.038 0.002 PHE D 88 TRP 0.018 0.002 TRP E 153 HIS 0.006 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00643 (17712) covalent geometry : angle 1.05667 (24030) SS BOND : bond 0.00757 ( 29) SS BOND : angle 9.07657 ( 58) hydrogen bonds : bond 0.24668 ( 630) hydrogen bonds : angle 8.45902 ( 1788) link_BETA1-4 : bond 0.00782 ( 12) link_BETA1-4 : angle 1.52386 ( 36) link_NAG-ASN : bond 0.00929 ( 24) link_NAG-ASN : angle 2.59840 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 385 time to evaluate : 0.688 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: L 3 GLN cc_start: 0.8545 (mp10) cc_final: 0.8251 (mp10) REVERT: L 32 TRP cc_start: 0.8833 (m-10) cc_final: 0.8153 (m-10) REVERT: L 82 ASP cc_start: 0.8918 (m-30) cc_final: 0.8663 (m-30) REVERT: H 33 CYS cc_start: 0.7487 (m) cc_final: 0.6197 (m) REVERT: H 39 GLN cc_start: 0.9200 (tt0) cc_final: 0.8509 (tm-30) REVERT: H 53 SER cc_start: 0.8908 (m) cc_final: 0.8671 (p) REVERT: H 60 ASN cc_start: 0.9302 (t0) cc_final: 0.8895 (t0) REVERT: H 72 ASP cc_start: 0.9122 (p0) cc_final: 0.8489 (p0) REVERT: H 78 PHE cc_start: 0.7779 (p90) cc_final: 0.7481 (p90) REVERT: H 95 GLU cc_start: 0.8915 (pm20) cc_final: 0.8119 (pm20) REVERT: H 100 ILE cc_start: 0.8643 (tp) cc_final: 0.8205 (tp) REVERT: A 14 CYS cc_start: 0.8833 (m) cc_final: 0.8233 (m) REVERT: A 190 ASP cc_start: 0.8957 (m-30) cc_final: 0.8748 (t0) REVERT: A 225 ASP cc_start: 0.8183 (t70) cc_final: 0.7946 (t0) REVERT: B 37 ASP cc_start: 0.8918 (t0) cc_final: 0.8568 (t0) REVERT: B 77 MET cc_start: 0.9168 (mmm) cc_final: 0.8888 (mmt) REVERT: B 112 ASP cc_start: 0.8804 (t0) cc_final: 0.8518 (t0) REVERT: B 149 MET cc_start: 0.9223 (mpp) cc_final: 0.9018 (mpp) REVERT: C 24 ASP cc_start: 0.8424 (m-30) cc_final: 0.8107 (m-30) REVERT: D 60 ASN cc_start: 0.7872 (t0) cc_final: 0.7042 (t0) REVERT: D 62 GLN cc_start: 0.8821 (mm110) cc_final: 0.8540 (mp-120) REVERT: D 109 ASP cc_start: 0.9032 (t0) cc_final: 0.8747 (t0) REVERT: D 113 SER cc_start: 0.9451 (t) cc_final: 0.9079 (p) REVERT: E 24 ASP cc_start: 0.8591 (m-30) cc_final: 0.8150 (p0) REVERT: E 152 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8806 (pp) REVERT: E 294 PHE cc_start: 0.9267 (m-80) cc_final: 0.8904 (m-80) REVERT: F 101 LEU cc_start: 0.9014 (mp) cc_final: 0.8790 (mt) REVERT: F 141 TYR cc_start: 0.7689 (m-80) cc_final: 0.7257 (m-80) REVERT: J 3 GLN cc_start: 0.8784 (mm110) cc_final: 0.8473 (mm-40) REVERT: J 47 LEU cc_start: 0.9144 (mp) cc_final: 0.8895 (mp) REVERT: G 46 GLU cc_start: 0.6840 (mp0) cc_final: 0.6249 (mp0) REVERT: G 59 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8793 (mm) REVERT: G 77 GLN cc_start: 0.8280 (pp30) cc_final: 0.7503 (pp30) REVERT: G 78 PHE cc_start: 0.7969 (p90) cc_final: 0.7429 (p90) outliers start: 7 outliers final: 0 residues processed: 388 average time/residue: 0.1201 time to fit residues: 72.6776 Evaluate side-chains 278 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 50 ASN B 111 HIS C 60 GLN C 196 HIS ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 79 ASN D 125 GLN E 141 HIS E 142 ASN E 158 ASN E 208 HIS E 285 GLN F 28 ASN F 142 HIS ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN K 27 GLN K 90 GLN I 3 GLN I 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049768 restraints weight = 61420.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051854 restraints weight = 30851.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053268 restraints weight = 20159.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054212 restraints weight = 15197.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054848 restraints weight = 12560.353| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17777 Z= 0.337 Angle : 0.770 10.510 24196 Z= 0.396 Chirality : 0.047 0.269 2721 Planarity : 0.005 0.050 3063 Dihedral : 7.607 62.144 3067 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 11.18 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2139 helix: 2.13 (0.26), residues: 381 sheet: 0.75 (0.23), residues: 522 loop : -0.69 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 106 TYR 0.027 0.002 TYR L 49 PHE 0.026 0.002 PHE C 147 TRP 0.026 0.002 TRP E 153 HIS 0.010 0.002 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00746 (17712) covalent geometry : angle 0.75566 (24030) SS BOND : bond 0.00682 ( 29) SS BOND : angle 1.63380 ( 58) hydrogen bonds : bond 0.05128 ( 630) hydrogen bonds : angle 6.10141 ( 1788) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 2.01955 ( 36) link_NAG-ASN : bond 0.00680 ( 24) link_NAG-ASN : angle 2.10978 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.679 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: L 3 GLN cc_start: 0.8563 (mp10) cc_final: 0.8243 (mp10) REVERT: L 32 TRP cc_start: 0.8694 (m-10) cc_final: 0.8132 (m-10) REVERT: H 39 GLN cc_start: 0.9282 (tt0) cc_final: 0.8857 (tt0) REVERT: H 60 ASN cc_start: 0.9279 (t0) cc_final: 0.8758 (t0) REVERT: H 105 GLN cc_start: 0.8944 (mm110) cc_final: 0.8639 (pp30) REVERT: A 14 CYS cc_start: 0.8667 (m) cc_final: 0.8001 (m) REVERT: A 53 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 225 ASP cc_start: 0.8254 (t70) cc_final: 0.7936 (t0) REVERT: B 42 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8799 (tt0) REVERT: B 90 ASP cc_start: 0.8689 (m-30) cc_final: 0.8348 (m-30) REVERT: B 106 ARG cc_start: 0.9537 (mmm-85) cc_final: 0.9247 (tpp80) REVERT: B 112 ASP cc_start: 0.8755 (t0) cc_final: 0.8535 (t0) REVERT: C 24 ASP cc_start: 0.8402 (m-30) cc_final: 0.8110 (m-30) REVERT: D 77 MET cc_start: 0.8626 (mtt) cc_final: 0.8235 (mtt) REVERT: D 109 ASP cc_start: 0.9002 (t0) cc_final: 0.8699 (t0) REVERT: D 113 SER cc_start: 0.9600 (t) cc_final: 0.9230 (p) REVERT: E 24 ASP cc_start: 0.8658 (m-30) cc_final: 0.8222 (p0) REVERT: E 98 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: F 28 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7147 (t0) REVERT: F 101 LEU cc_start: 0.8957 (mp) cc_final: 0.8605 (mt) REVERT: F 113 SER cc_start: 0.9629 (t) cc_final: 0.9254 (p) REVERT: F 141 TYR cc_start: 0.7945 (m-80) cc_final: 0.7406 (m-80) REVERT: J 47 LEU cc_start: 0.9306 (mp) cc_final: 0.8904 (mp) REVERT: G 46 GLU cc_start: 0.7361 (mp0) cc_final: 0.6600 (mp0) REVERT: G 77 GLN cc_start: 0.8265 (pp30) cc_final: 0.7567 (pp30) REVERT: K 4 MET cc_start: 0.8925 (mmm) cc_final: 0.8668 (mmm) outliers start: 43 outliers final: 19 residues processed: 303 average time/residue: 0.1102 time to fit residues: 53.4479 Evaluate side-chains 256 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 158 ASN F 169 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN K 6 GLN K 38 GLN K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051467 restraints weight = 60661.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053661 restraints weight = 29663.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055144 restraints weight = 19000.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056117 restraints weight = 14136.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056829 restraints weight = 11595.274| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17777 Z= 0.131 Angle : 0.609 10.657 24196 Z= 0.310 Chirality : 0.044 0.251 2721 Planarity : 0.004 0.043 3063 Dihedral : 6.137 58.344 3063 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.70 % Allowed : 13.58 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2139 helix: 2.44 (0.27), residues: 375 sheet: 1.06 (0.23), residues: 510 loop : -0.62 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 50 TYR 0.024 0.001 TYR C 168 PHE 0.021 0.002 PHE I 78 TRP 0.021 0.001 TRP K 32 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00293 (17712) covalent geometry : angle 0.59568 (24030) SS BOND : bond 0.00374 ( 29) SS BOND : angle 1.76189 ( 58) hydrogen bonds : bond 0.04910 ( 630) hydrogen bonds : angle 5.51437 ( 1788) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 1.61437 ( 36) link_NAG-ASN : bond 0.00192 ( 24) link_NAG-ASN : angle 1.54416 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.693 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: L 3 GLN cc_start: 0.8507 (mp10) cc_final: 0.7970 (mp10) REVERT: L 27 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8338 (mm-40) REVERT: L 98 PHE cc_start: 0.8340 (m-80) cc_final: 0.8129 (m-10) REVERT: H 39 GLN cc_start: 0.9284 (tt0) cc_final: 0.8505 (tm-30) REVERT: H 60 ASN cc_start: 0.9256 (t0) cc_final: 0.8746 (t0) REVERT: H 100 ILE cc_start: 0.8865 (tp) cc_final: 0.8661 (mp) REVERT: H 105 GLN cc_start: 0.8949 (mm110) cc_final: 0.8599 (pp30) REVERT: A 14 CYS cc_start: 0.8723 (m) cc_final: 0.8010 (m) REVERT: A 225 ASP cc_start: 0.8115 (t70) cc_final: 0.7777 (t0) REVERT: A 265 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 90 ASP cc_start: 0.8680 (m-30) cc_final: 0.8262 (m-30) REVERT: B 112 ASP cc_start: 0.8703 (t0) cc_final: 0.8494 (t0) REVERT: C 24 ASP cc_start: 0.8457 (m-30) cc_final: 0.8124 (m-30) REVERT: C 278 ASP cc_start: 0.8984 (t70) cc_final: 0.8724 (t0) REVERT: D 17 MET cc_start: 0.8843 (ttp) cc_final: 0.8630 (ppp) REVERT: D 77 MET cc_start: 0.8580 (mtt) cc_final: 0.8172 (mtt) REVERT: D 106 ARG cc_start: 0.9056 (ttm-80) cc_final: 0.8605 (ttm-80) REVERT: D 109 ASP cc_start: 0.8966 (t0) cc_final: 0.8452 (t0) REVERT: D 112 ASP cc_start: 0.8971 (m-30) cc_final: 0.8613 (p0) REVERT: D 113 SER cc_start: 0.9563 (t) cc_final: 0.8921 (p) REVERT: E 24 ASP cc_start: 0.8557 (m-30) cc_final: 0.8221 (p0) REVERT: E 98 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: F 42 GLN cc_start: 0.8659 (tt0) cc_final: 0.8119 (tm-30) REVERT: F 101 LEU cc_start: 0.8862 (mp) cc_final: 0.8417 (mt) REVERT: F 113 SER cc_start: 0.9603 (t) cc_final: 0.9203 (p) REVERT: F 141 TYR cc_start: 0.7766 (m-80) cc_final: 0.7345 (m-80) REVERT: J 36 TYR cc_start: 0.8228 (m-80) cc_final: 0.7883 (m-10) REVERT: J 47 LEU cc_start: 0.9301 (mp) cc_final: 0.8952 (mp) REVERT: G 72 ASP cc_start: 0.7667 (m-30) cc_final: 0.6951 (m-30) REVERT: G 75 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8658 (mppt) REVERT: G 77 GLN cc_start: 0.8307 (pp30) cc_final: 0.7606 (pp30) REVERT: I 100 PHE cc_start: 0.9039 (m-80) cc_final: 0.8761 (m-80) outliers start: 32 outliers final: 14 residues processed: 299 average time/residue: 0.1078 time to fit residues: 51.9441 Evaluate side-chains 263 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain G residue 82 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 18 optimal weight: 0.0010 chunk 205 optimal weight: 0.8980 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN D 50 ASN D 62 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 90 GLN ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.046922 restraints weight = 61595.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.048990 restraints weight = 30587.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050377 restraints weight = 19850.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.051343 restraints weight = 14956.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052001 restraints weight = 12294.503| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17777 Z= 0.251 Angle : 0.675 15.980 24196 Z= 0.341 Chirality : 0.045 0.249 2721 Planarity : 0.004 0.044 3063 Dihedral : 5.597 58.308 3063 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.56 % Allowed : 14.80 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2139 helix: 2.32 (0.27), residues: 375 sheet: 0.76 (0.24), residues: 501 loop : -0.75 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100F TYR 0.018 0.002 TYR C 168 PHE 0.020 0.002 PHE I 78 TRP 0.021 0.001 TRP K 32 HIS 0.006 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00561 (17712) covalent geometry : angle 0.66179 (24030) SS BOND : bond 0.00511 ( 29) SS BOND : angle 1.68140 ( 58) hydrogen bonds : bond 0.04712 ( 630) hydrogen bonds : angle 5.47263 ( 1788) link_BETA1-4 : bond 0.00299 ( 12) link_BETA1-4 : angle 1.58763 ( 36) link_NAG-ASN : bond 0.00513 ( 24) link_NAG-ASN : angle 1.81235 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.663 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: L 3 GLN cc_start: 0.8531 (mp10) cc_final: 0.8102 (mp10) REVERT: L 32 TRP cc_start: 0.8724 (m-10) cc_final: 0.8435 (m-10) REVERT: L 70 ASP cc_start: 0.9035 (t0) cc_final: 0.8788 (p0) REVERT: H 60 ASN cc_start: 0.9276 (t0) cc_final: 0.8732 (t0) REVERT: A 14 CYS cc_start: 0.8699 (m) cc_final: 0.7870 (m) REVERT: A 265 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 59 MET cc_start: 0.8647 (tpp) cc_final: 0.8416 (tpp) REVERT: C 24 ASP cc_start: 0.8517 (m-30) cc_final: 0.8186 (m-30) REVERT: D 17 MET cc_start: 0.8995 (ttp) cc_final: 0.8670 (ppp) REVERT: D 59 MET cc_start: 0.9208 (tpp) cc_final: 0.8560 (tpp) REVERT: D 109 ASP cc_start: 0.9126 (t0) cc_final: 0.8811 (t0) REVERT: D 112 ASP cc_start: 0.9140 (m-30) cc_final: 0.8699 (t0) REVERT: E 24 ASP cc_start: 0.8722 (m-30) cc_final: 0.8185 (p0) REVERT: E 98 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: F 17 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7341 (ttp) REVERT: F 101 LEU cc_start: 0.8870 (mp) cc_final: 0.8483 (mt) REVERT: F 113 SER cc_start: 0.9634 (t) cc_final: 0.9264 (p) REVERT: F 141 TYR cc_start: 0.8233 (m-80) cc_final: 0.7651 (m-80) REVERT: J 47 LEU cc_start: 0.9291 (mp) cc_final: 0.8824 (mp) REVERT: G 46 GLU cc_start: 0.7319 (mp0) cc_final: 0.7010 (mp0) REVERT: G 72 ASP cc_start: 0.7996 (m-30) cc_final: 0.7578 (m-30) REVERT: G 77 GLN cc_start: 0.8292 (pp30) cc_final: 0.7629 (pp30) REVERT: G 87 THR cc_start: 0.8969 (t) cc_final: 0.8661 (m) REVERT: G 100 ILE cc_start: 0.9354 (mm) cc_final: 0.9046 (mp) REVERT: K 27 GLN cc_start: 0.8423 (mt0) cc_final: 0.8143 (pt0) REVERT: K 38 GLN cc_start: 0.8688 (tt0) cc_final: 0.8478 (tm-30) REVERT: I 100 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8601 (mmp80) outliers start: 48 outliers final: 30 residues processed: 286 average time/residue: 0.1129 time to fit residues: 51.8464 Evaluate side-chains 254 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 0.0870 chunk 95 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.048673 restraints weight = 59921.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050795 restraints weight = 29456.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052256 restraints weight = 19010.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053213 restraints weight = 14219.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053903 restraints weight = 11700.879| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17777 Z= 0.125 Angle : 0.588 9.954 24196 Z= 0.298 Chirality : 0.043 0.243 2721 Planarity : 0.004 0.053 3063 Dihedral : 5.133 55.783 3063 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.08 % Allowed : 15.71 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2139 helix: 2.49 (0.27), residues: 375 sheet: 1.03 (0.24), residues: 489 loop : -0.70 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 100F TYR 0.014 0.001 TYR L 49 PHE 0.017 0.002 PHE I 100 TRP 0.016 0.001 TRP K 32 HIS 0.002 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00283 (17712) covalent geometry : angle 0.57603 (24030) SS BOND : bond 0.00399 ( 29) SS BOND : angle 1.59350 ( 58) hydrogen bonds : bond 0.04475 ( 630) hydrogen bonds : angle 5.12918 ( 1788) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.38743 ( 36) link_NAG-ASN : bond 0.00192 ( 24) link_NAG-ASN : angle 1.55108 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8496 (mp10) cc_final: 0.7909 (mp10) REVERT: L 24 ARG cc_start: 0.9336 (ttt90) cc_final: 0.9056 (ttm-80) REVERT: L 27 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8309 (mm-40) REVERT: L 70 ASP cc_start: 0.9055 (t0) cc_final: 0.8827 (p0) REVERT: H 60 ASN cc_start: 0.9272 (t0) cc_final: 0.8758 (t0) REVERT: H 100 ILE cc_start: 0.8903 (tp) cc_final: 0.8664 (mp) REVERT: A 14 CYS cc_start: 0.8806 (m) cc_final: 0.8009 (m) REVERT: A 265 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.7955 (t) REVERT: B 59 MET cc_start: 0.8559 (tpp) cc_final: 0.8329 (tpp) REVERT: B 90 ASP cc_start: 0.8838 (m-30) cc_final: 0.8476 (m-30) REVERT: B 149 MET cc_start: 0.9111 (mpp) cc_final: 0.8825 (mmt) REVERT: C 24 ASP cc_start: 0.8531 (m-30) cc_final: 0.8209 (m-30) REVERT: D 77 MET cc_start: 0.8500 (mtt) cc_final: 0.8036 (mtt) REVERT: D 106 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8902 (ttm-80) REVERT: D 109 ASP cc_start: 0.9089 (t0) cc_final: 0.8661 (t0) REVERT: D 112 ASP cc_start: 0.9117 (m-30) cc_final: 0.8715 (p0) REVERT: D 113 SER cc_start: 0.9572 (t) cc_final: 0.8852 (p) REVERT: D 140 PHE cc_start: 0.8607 (m-80) cc_final: 0.8278 (m-80) REVERT: E 24 ASP cc_start: 0.8698 (m-30) cc_final: 0.8279 (p0) REVERT: E 98 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: F 17 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7102 (ttp) REVERT: F 42 GLN cc_start: 0.8833 (tt0) cc_final: 0.8423 (tt0) REVERT: F 101 LEU cc_start: 0.8803 (mp) cc_final: 0.8467 (mt) REVERT: F 113 SER cc_start: 0.9618 (t) cc_final: 0.9242 (p) REVERT: F 141 TYR cc_start: 0.8146 (m-80) cc_final: 0.7622 (m-80) REVERT: J 27 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8622 (tp40) REVERT: J 42 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8630 (mmmm) REVERT: J 47 LEU cc_start: 0.9279 (mp) cc_final: 0.8910 (mp) REVERT: G 16 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 46 GLU cc_start: 0.7300 (mp0) cc_final: 0.6971 (mp0) REVERT: G 72 ASP cc_start: 0.7947 (m-30) cc_final: 0.7174 (m-30) REVERT: G 75 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8594 (mppt) REVERT: G 77 GLN cc_start: 0.8279 (pp30) cc_final: 0.7634 (pp30) REVERT: G 87 THR cc_start: 0.8961 (t) cc_final: 0.8656 (m) REVERT: G 100 ILE cc_start: 0.9244 (mm) cc_final: 0.8945 (mp) outliers start: 39 outliers final: 24 residues processed: 291 average time/residue: 0.1105 time to fit residues: 51.0783 Evaluate side-chains 265 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 192 optimal weight: 0.0970 chunk 187 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 46 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.047860 restraints weight = 60527.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.049948 restraints weight = 30062.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.051389 restraints weight = 19522.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052309 restraints weight = 14683.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053007 restraints weight = 12151.334| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17777 Z= 0.170 Angle : 0.616 11.764 24196 Z= 0.310 Chirality : 0.043 0.245 2721 Planarity : 0.004 0.054 3063 Dihedral : 5.075 56.030 3063 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.24 % Allowed : 16.56 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2139 helix: 2.49 (0.27), residues: 375 sheet: 0.88 (0.24), residues: 495 loop : -0.68 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 24 TYR 0.016 0.001 TYR D 119 PHE 0.021 0.002 PHE L 98 TRP 0.015 0.001 TRP K 32 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00386 (17712) covalent geometry : angle 0.60267 (24030) SS BOND : bond 0.00346 ( 29) SS BOND : angle 1.78260 ( 58) hydrogen bonds : bond 0.04387 ( 630) hydrogen bonds : angle 5.14808 ( 1788) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.41668 ( 36) link_NAG-ASN : bond 0.00293 ( 24) link_NAG-ASN : angle 1.61631 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8495 (mp10) cc_final: 0.7906 (mp10) REVERT: L 24 ARG cc_start: 0.9354 (ttt90) cc_final: 0.9088 (ttm-80) REVERT: L 27 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8345 (mm-40) REVERT: L 70 ASP cc_start: 0.9057 (t0) cc_final: 0.8857 (p0) REVERT: L 78 LEU cc_start: 0.9017 (tt) cc_final: 0.8712 (tt) REVERT: H 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8741 (t0) REVERT: H 100 ILE cc_start: 0.8927 (tp) cc_final: 0.8638 (mp) REVERT: H 100 ARG cc_start: 0.7763 (mmp80) cc_final: 0.7530 (mmp80) REVERT: A 14 CYS cc_start: 0.8782 (m) cc_final: 0.8011 (m) REVERT: A 24 ASP cc_start: 0.9127 (m-30) cc_final: 0.8875 (m-30) REVERT: A 265 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 90 ASP cc_start: 0.8857 (m-30) cc_final: 0.8493 (m-30) REVERT: B 149 MET cc_start: 0.9104 (mpp) cc_final: 0.8804 (mmt) REVERT: C 24 ASP cc_start: 0.8537 (m-30) cc_final: 0.8224 (m-30) REVERT: D 58 LYS cc_start: 0.9493 (mmmt) cc_final: 0.9217 (mmmm) REVERT: D 59 MET cc_start: 0.9207 (tpp) cc_final: 0.8674 (tpp) REVERT: D 77 MET cc_start: 0.8567 (mtt) cc_final: 0.8134 (mtt) REVERT: D 97 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: D 106 ARG cc_start: 0.9187 (ttm-80) cc_final: 0.8811 (ttm-80) REVERT: D 109 ASP cc_start: 0.9095 (t0) cc_final: 0.8661 (t0) REVERT: D 112 ASP cc_start: 0.9125 (m-30) cc_final: 0.8717 (p0) REVERT: D 113 SER cc_start: 0.9582 (t) cc_final: 0.8842 (p) REVERT: D 140 PHE cc_start: 0.8775 (m-80) cc_final: 0.8421 (m-80) REVERT: E 24 ASP cc_start: 0.8743 (m-30) cc_final: 0.8356 (p0) REVERT: E 98 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: F 17 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7087 (ttp) REVERT: F 101 LEU cc_start: 0.8901 (mp) cc_final: 0.8505 (mt) REVERT: F 105 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8579 (mm-30) REVERT: F 113 SER cc_start: 0.9627 (t) cc_final: 0.9288 (p) REVERT: F 141 TYR cc_start: 0.8254 (m-80) cc_final: 0.7702 (m-80) REVERT: J 27 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8670 (tp40) REVERT: J 47 LEU cc_start: 0.9256 (mp) cc_final: 0.8820 (mp) REVERT: G 16 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: G 46 GLU cc_start: 0.7362 (mp0) cc_final: 0.7039 (mp0) REVERT: G 72 ASP cc_start: 0.7972 (m-30) cc_final: 0.7196 (m-30) REVERT: G 75 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8608 (mppt) REVERT: G 77 GLN cc_start: 0.8330 (pp30) cc_final: 0.7686 (pp30) REVERT: G 87 THR cc_start: 0.8905 (t) cc_final: 0.8608 (m) REVERT: K 27 GLN cc_start: 0.8421 (mt0) cc_final: 0.8183 (pt0) outliers start: 42 outliers final: 24 residues processed: 279 average time/residue: 0.1132 time to fit residues: 50.1675 Evaluate side-chains 265 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.047996 restraints weight = 60769.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.050115 restraints weight = 29853.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.051578 restraints weight = 19229.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.052552 restraints weight = 14391.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053120 restraints weight = 11792.476| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17777 Z= 0.149 Angle : 0.606 11.561 24196 Z= 0.305 Chirality : 0.043 0.242 2721 Planarity : 0.004 0.056 3063 Dihedral : 4.937 55.616 3063 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.13 % Allowed : 17.47 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2139 helix: 2.49 (0.27), residues: 375 sheet: 0.87 (0.24), residues: 495 loop : -0.65 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.017 0.001 TYR D 119 PHE 0.017 0.001 PHE H 78 TRP 0.017 0.001 TRP L 32 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00341 (17712) covalent geometry : angle 0.59383 (24030) SS BOND : bond 0.00364 ( 29) SS BOND : angle 1.66798 ( 58) hydrogen bonds : bond 0.04311 ( 630) hydrogen bonds : angle 5.03192 ( 1788) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.36927 ( 36) link_NAG-ASN : bond 0.00227 ( 24) link_NAG-ASN : angle 1.57402 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8458 (mp10) cc_final: 0.8032 (mp10) REVERT: L 24 ARG cc_start: 0.9359 (ttt90) cc_final: 0.9106 (ttm-80) REVERT: L 32 TRP cc_start: 0.8771 (m-10) cc_final: 0.8101 (m-10) REVERT: L 78 LEU cc_start: 0.9049 (tt) cc_final: 0.8751 (tt) REVERT: H 56 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.7898 (t) REVERT: H 60 ASN cc_start: 0.9278 (t0) cc_final: 0.8762 (t0) REVERT: H 95 GLU cc_start: 0.7102 (pm20) cc_final: 0.6725 (pm20) REVERT: A 14 CYS cc_start: 0.8763 (m) cc_final: 0.8004 (m) REVERT: A 265 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7914 (t) REVERT: A 305 CYS cc_start: 0.5632 (p) cc_final: 0.5360 (p) REVERT: B 90 ASP cc_start: 0.8861 (m-30) cc_final: 0.8491 (m-30) REVERT: B 149 MET cc_start: 0.9128 (mpp) cc_final: 0.8777 (mmt) REVERT: C 24 ASP cc_start: 0.8546 (m-30) cc_final: 0.8242 (m-30) REVERT: D 58 LYS cc_start: 0.9494 (mmmt) cc_final: 0.9249 (mmmm) REVERT: D 59 MET cc_start: 0.9199 (tpp) cc_final: 0.8280 (tpp) REVERT: D 77 MET cc_start: 0.8598 (mtt) cc_final: 0.8147 (mtt) REVERT: D 97 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: D 106 ARG cc_start: 0.9190 (ttm-80) cc_final: 0.8816 (ttm-80) REVERT: D 109 ASP cc_start: 0.9067 (t0) cc_final: 0.8626 (t0) REVERT: D 112 ASP cc_start: 0.9130 (m-30) cc_final: 0.8739 (p0) REVERT: D 113 SER cc_start: 0.9581 (t) cc_final: 0.8841 (p) REVERT: D 140 PHE cc_start: 0.8739 (m-80) cc_final: 0.8366 (m-80) REVERT: E 24 ASP cc_start: 0.8717 (m-30) cc_final: 0.8340 (p0) REVERT: E 98 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: F 17 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6929 (ttp) REVERT: F 101 LEU cc_start: 0.8859 (mp) cc_final: 0.8453 (mt) REVERT: F 105 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8586 (mm-30) REVERT: F 113 SER cc_start: 0.9623 (t) cc_final: 0.9277 (p) REVERT: F 141 TYR cc_start: 0.8304 (m-80) cc_final: 0.7749 (m-80) REVERT: J 27 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8711 (tp40) REVERT: J 47 LEU cc_start: 0.9267 (mp) cc_final: 0.8919 (mp) REVERT: G 5 GLN cc_start: 0.8352 (tm130) cc_final: 0.8046 (tm-30) REVERT: G 46 GLU cc_start: 0.7385 (mp0) cc_final: 0.7084 (mp0) REVERT: G 72 ASP cc_start: 0.7984 (m-30) cc_final: 0.7225 (m-30) REVERT: G 75 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8628 (mppt) REVERT: G 77 GLN cc_start: 0.8341 (pp30) cc_final: 0.7700 (pp30) REVERT: G 87 THR cc_start: 0.8890 (t) cc_final: 0.8606 (m) REVERT: K 27 GLN cc_start: 0.8453 (mt0) cc_final: 0.8213 (pt0) outliers start: 40 outliers final: 24 residues processed: 274 average time/residue: 0.1144 time to fit residues: 49.9614 Evaluate side-chains 264 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.047805 restraints weight = 60935.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049899 restraints weight = 30313.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.051296 restraints weight = 19642.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052270 restraints weight = 14786.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.052903 restraints weight = 12125.621| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17777 Z= 0.164 Angle : 0.632 12.111 24196 Z= 0.317 Chirality : 0.043 0.242 2721 Planarity : 0.004 0.056 3063 Dihedral : 4.950 55.861 3063 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.92 % Allowed : 17.84 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2139 helix: 2.41 (0.27), residues: 381 sheet: 0.73 (0.24), residues: 501 loop : -0.64 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 100F TYR 0.016 0.001 TYR D 119 PHE 0.016 0.001 PHE I 78 TRP 0.013 0.001 TRP K 32 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00373 (17712) covalent geometry : angle 0.61664 (24030) SS BOND : bond 0.00333 ( 29) SS BOND : angle 2.19056 ( 58) hydrogen bonds : bond 0.04283 ( 630) hydrogen bonds : angle 5.06900 ( 1788) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 1.36937 ( 36) link_NAG-ASN : bond 0.00262 ( 24) link_NAG-ASN : angle 1.59613 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8439 (mp10) cc_final: 0.7829 (mp10) REVERT: L 27 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7931 (mp10) REVERT: L 32 TRP cc_start: 0.8759 (m-10) cc_final: 0.8147 (m100) REVERT: L 78 LEU cc_start: 0.9054 (tt) cc_final: 0.8749 (tt) REVERT: H 33 CYS cc_start: 0.7575 (m) cc_final: 0.6786 (m) REVERT: H 60 ASN cc_start: 0.9291 (t0) cc_final: 0.8791 (t0) REVERT: H 95 GLU cc_start: 0.7125 (pm20) cc_final: 0.6885 (pm20) REVERT: A 14 CYS cc_start: 0.8742 (m) cc_final: 0.8000 (m) REVERT: A 265 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7980 (t) REVERT: B 90 ASP cc_start: 0.8829 (m-30) cc_final: 0.8479 (m-30) REVERT: B 106 ARG cc_start: 0.9517 (mmm-85) cc_final: 0.9189 (tpp80) REVERT: B 149 MET cc_start: 0.9137 (mpp) cc_final: 0.8828 (mmt) REVERT: C 24 ASP cc_start: 0.8522 (m-30) cc_final: 0.8226 (m-30) REVERT: D 77 MET cc_start: 0.8628 (mtt) cc_final: 0.8162 (mtt) REVERT: D 97 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: D 106 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8233 (ttm-80) REVERT: D 109 ASP cc_start: 0.8986 (t0) cc_final: 0.8572 (t0) REVERT: D 112 ASP cc_start: 0.9098 (m-30) cc_final: 0.8718 (p0) REVERT: D 113 SER cc_start: 0.9587 (t) cc_final: 0.8840 (p) REVERT: D 140 PHE cc_start: 0.8754 (m-80) cc_final: 0.8370 (m-80) REVERT: E 24 ASP cc_start: 0.8636 (m-30) cc_final: 0.8341 (p0) REVERT: E 98 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: F 17 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6979 (ttp) REVERT: F 101 LEU cc_start: 0.8896 (mp) cc_final: 0.8490 (mt) REVERT: F 105 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8613 (mm-30) REVERT: F 113 SER cc_start: 0.9627 (t) cc_final: 0.9279 (p) REVERT: F 141 TYR cc_start: 0.8307 (m-80) cc_final: 0.7779 (m-80) REVERT: J 27 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8761 (tp40) REVERT: J 47 LEU cc_start: 0.9279 (mp) cc_final: 0.8864 (mp) REVERT: G 5 GLN cc_start: 0.8314 (tm130) cc_final: 0.8007 (tm-30) REVERT: G 46 GLU cc_start: 0.7513 (mp0) cc_final: 0.7206 (mp0) REVERT: G 72 ASP cc_start: 0.7983 (m-30) cc_final: 0.7257 (m-30) REVERT: G 75 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8700 (mppt) REVERT: G 77 GLN cc_start: 0.8402 (pp30) cc_final: 0.7771 (pp30) REVERT: G 87 THR cc_start: 0.8904 (t) cc_final: 0.8641 (m) REVERT: K 27 GLN cc_start: 0.8502 (mt0) cc_final: 0.8268 (pt0) REVERT: K 38 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7759 (tp40) REVERT: I 3 GLN cc_start: 0.8178 (mm110) cc_final: 0.7876 (mm-40) outliers start: 36 outliers final: 25 residues processed: 269 average time/residue: 0.1119 time to fit residues: 48.1337 Evaluate side-chains 262 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.047313 restraints weight = 61290.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.049387 restraints weight = 30504.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050798 restraints weight = 19805.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051740 restraints weight = 14872.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.052356 restraints weight = 12251.497| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17777 Z= 0.189 Angle : 0.641 12.365 24196 Z= 0.324 Chirality : 0.044 0.243 2721 Planarity : 0.004 0.057 3063 Dihedral : 4.918 56.124 3063 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.13 % Allowed : 17.78 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2139 helix: 2.38 (0.27), residues: 375 sheet: 0.81 (0.24), residues: 489 loop : -0.69 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100F TYR 0.011 0.001 TYR L 49 PHE 0.024 0.002 PHE H 78 TRP 0.032 0.001 TRP L 32 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00428 (17712) covalent geometry : angle 0.63000 (24030) SS BOND : bond 0.00442 ( 29) SS BOND : angle 1.60381 ( 58) hydrogen bonds : bond 0.04365 ( 630) hydrogen bonds : angle 5.03053 ( 1788) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.36455 ( 36) link_NAG-ASN : bond 0.00316 ( 24) link_NAG-ASN : angle 1.64302 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8443 (mp10) cc_final: 0.7923 (mp10) REVERT: L 27 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8417 (mm-40) REVERT: L 78 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8780 (tt) REVERT: H 33 CYS cc_start: 0.7573 (m) cc_final: 0.6985 (m) REVERT: H 56 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.7929 (t) REVERT: H 60 ASN cc_start: 0.9295 (t0) cc_final: 0.8759 (t0) REVERT: H 100 ILE cc_start: 0.8642 (tp) cc_final: 0.8441 (mp) REVERT: A 14 CYS cc_start: 0.8786 (m) cc_final: 0.8038 (m) REVERT: A 265 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7917 (t) REVERT: B 90 ASP cc_start: 0.8880 (m-30) cc_final: 0.8524 (m-30) REVERT: B 106 ARG cc_start: 0.9514 (mmm-85) cc_final: 0.9186 (tpp80) REVERT: B 149 MET cc_start: 0.9133 (mpp) cc_final: 0.8807 (mmt) REVERT: C 24 ASP cc_start: 0.8559 (m-30) cc_final: 0.8252 (m-30) REVERT: D 77 MET cc_start: 0.8643 (mtt) cc_final: 0.8184 (mtt) REVERT: D 97 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7995 (tp30) REVERT: D 106 ARG cc_start: 0.9205 (ttm-80) cc_final: 0.8320 (ttm-80) REVERT: D 109 ASP cc_start: 0.9057 (t0) cc_final: 0.8632 (t0) REVERT: D 112 ASP cc_start: 0.9145 (m-30) cc_final: 0.8719 (p0) REVERT: D 113 SER cc_start: 0.9586 (t) cc_final: 0.8846 (p) REVERT: E 24 ASP cc_start: 0.8734 (m-30) cc_final: 0.8355 (p0) REVERT: E 98 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: F 17 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6845 (ttp) REVERT: F 53 ASN cc_start: 0.8999 (m-40) cc_final: 0.8792 (m-40) REVERT: F 101 LEU cc_start: 0.8851 (mp) cc_final: 0.8453 (mt) REVERT: F 105 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8606 (mm-30) REVERT: F 113 SER cc_start: 0.9637 (t) cc_final: 0.9297 (p) REVERT: F 141 TYR cc_start: 0.8390 (m-80) cc_final: 0.7804 (m-80) REVERT: J 27 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8758 (tp40) REVERT: J 47 LEU cc_start: 0.9239 (mp) cc_final: 0.8871 (mp) REVERT: G 1 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8157 (tm-30) REVERT: G 3 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8427 (mm-40) REVERT: G 5 GLN cc_start: 0.8329 (tm130) cc_final: 0.8015 (tm-30) REVERT: G 46 GLU cc_start: 0.7601 (mp0) cc_final: 0.7303 (mp0) REVERT: G 72 ASP cc_start: 0.8042 (m-30) cc_final: 0.7294 (m-30) REVERT: G 75 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8694 (mppt) REVERT: G 77 GLN cc_start: 0.8402 (pp30) cc_final: 0.7782 (pp30) REVERT: G 87 THR cc_start: 0.8884 (t) cc_final: 0.8591 (m) REVERT: K 27 GLN cc_start: 0.8505 (mt0) cc_final: 0.8232 (pt0) REVERT: I 3 GLN cc_start: 0.8173 (mm110) cc_final: 0.7870 (mm-40) outliers start: 40 outliers final: 27 residues processed: 267 average time/residue: 0.1133 time to fit residues: 48.6173 Evaluate side-chains 265 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 195 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.048312 restraints weight = 60043.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050431 restraints weight = 29690.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051868 restraints weight = 19195.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.052840 restraints weight = 14359.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.053504 restraints weight = 11761.613| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17777 Z= 0.126 Angle : 0.647 13.064 24196 Z= 0.322 Chirality : 0.044 0.239 2721 Planarity : 0.004 0.055 3063 Dihedral : 4.862 55.330 3063 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.70 % Allowed : 18.42 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2139 helix: 2.33 (0.27), residues: 381 sheet: 0.71 (0.24), residues: 477 loop : -0.65 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100F TYR 0.018 0.001 TYR D 119 PHE 0.016 0.001 PHE I 78 TRP 0.018 0.001 TRP L 32 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00290 (17712) covalent geometry : angle 0.63312 (24030) SS BOND : bond 0.00296 ( 29) SS BOND : angle 2.09079 ( 58) hydrogen bonds : bond 0.04264 ( 630) hydrogen bonds : angle 5.02153 ( 1788) link_BETA1-4 : bond 0.00384 ( 12) link_BETA1-4 : angle 1.34645 ( 36) link_NAG-ASN : bond 0.00177 ( 24) link_NAG-ASN : angle 1.55084 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8416 (mp10) cc_final: 0.7847 (mp10) REVERT: L 11 LEU cc_start: 0.8263 (mt) cc_final: 0.7960 (mp) REVERT: L 27 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8010 (mp10) REVERT: L 32 TRP cc_start: 0.8579 (m-10) cc_final: 0.8201 (m100) REVERT: L 78 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8838 (tt) REVERT: H 33 CYS cc_start: 0.7601 (m) cc_final: 0.7078 (m) REVERT: H 56 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.7876 (t) REVERT: H 60 ASN cc_start: 0.9292 (t0) cc_final: 0.8774 (t0) REVERT: A 14 CYS cc_start: 0.8723 (m) cc_final: 0.7986 (m) REVERT: A 265 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 90 ASP cc_start: 0.8874 (m-30) cc_final: 0.8501 (m-30) REVERT: B 149 MET cc_start: 0.9132 (mpp) cc_final: 0.8821 (mmt) REVERT: B 168 LEU cc_start: 0.9812 (tt) cc_final: 0.9546 (pp) REVERT: C 24 ASP cc_start: 0.8553 (m-30) cc_final: 0.8246 (m-30) REVERT: D 77 MET cc_start: 0.8621 (mtt) cc_final: 0.8135 (mtt) REVERT: D 97 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: D 106 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8844 (ttm-80) REVERT: D 109 ASP cc_start: 0.9036 (t0) cc_final: 0.8527 (t0) REVERT: D 112 ASP cc_start: 0.9115 (m-30) cc_final: 0.8653 (p0) REVERT: D 113 SER cc_start: 0.9567 (t) cc_final: 0.8821 (p) REVERT: E 24 ASP cc_start: 0.8696 (m-30) cc_final: 0.8364 (p0) REVERT: E 98 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: F 17 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6645 (ttp) REVERT: F 53 ASN cc_start: 0.8978 (m-40) cc_final: 0.8770 (m-40) REVERT: F 101 LEU cc_start: 0.8819 (mp) cc_final: 0.8424 (mt) REVERT: F 105 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8615 (mm-30) REVERT: F 113 SER cc_start: 0.9608 (t) cc_final: 0.9221 (p) REVERT: F 141 TYR cc_start: 0.8327 (m-80) cc_final: 0.7808 (m-80) REVERT: J 27 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8759 (tp40) REVERT: J 47 LEU cc_start: 0.9256 (mp) cc_final: 0.8838 (mp) REVERT: G 1 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8427 (tm-30) REVERT: G 5 GLN cc_start: 0.8352 (tm130) cc_final: 0.8132 (tm-30) REVERT: G 46 GLU cc_start: 0.7575 (mp0) cc_final: 0.7276 (mp0) REVERT: G 72 ASP cc_start: 0.8058 (m-30) cc_final: 0.7326 (m-30) REVERT: G 75 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8691 (mppt) REVERT: G 77 GLN cc_start: 0.8406 (pp30) cc_final: 0.7847 (pp30) REVERT: G 87 THR cc_start: 0.8885 (t) cc_final: 0.8580 (m) REVERT: G 105 GLN cc_start: 0.8496 (mt0) cc_final: 0.8261 (mp10) REVERT: K 27 GLN cc_start: 0.8536 (mt0) cc_final: 0.8251 (pt0) REVERT: I 3 GLN cc_start: 0.8173 (mm110) cc_final: 0.7873 (mm-40) outliers start: 32 outliers final: 21 residues processed: 272 average time/residue: 0.1193 time to fit residues: 51.4894 Evaluate side-chains 265 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 17 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.048713 restraints weight = 59984.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050842 restraints weight = 29624.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052293 restraints weight = 19042.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.053280 restraints weight = 14202.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053976 restraints weight = 11598.925| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17777 Z= 0.123 Angle : 0.636 13.230 24196 Z= 0.315 Chirality : 0.043 0.239 2721 Planarity : 0.004 0.069 3063 Dihedral : 4.774 55.601 3063 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.49 % Allowed : 18.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2139 helix: 2.34 (0.27), residues: 381 sheet: 0.78 (0.24), residues: 486 loop : -0.62 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 262 TYR 0.018 0.001 TYR D 119 PHE 0.025 0.001 PHE H 78 TRP 0.015 0.001 TRP L 32 HIS 0.002 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00284 (17712) covalent geometry : angle 0.62352 (24030) SS BOND : bond 0.00340 ( 29) SS BOND : angle 1.90958 ( 58) hydrogen bonds : bond 0.04146 ( 630) hydrogen bonds : angle 4.99302 ( 1788) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.34225 ( 36) link_NAG-ASN : bond 0.00156 ( 24) link_NAG-ASN : angle 1.52299 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.24 seconds wall clock time: 45 minutes 24.85 seconds (2724.85 seconds total)