Starting phenix.real_space_refine on Sat Sep 12 18:17:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xsk_22302/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xsk_22302/09_2026/6xsk_22302.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.92, per 1000 atoms: 0.23 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: 1.48 Conformation dependent library (CDL) restraints added in 586.0 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: 0.44 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: 2.79 Time building geometry restraints manager: 1.89 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 - 17.67: 9373 17.67 - 35.34: 743 35.34 - 53.01: 150 53.01 - 70.68: 19 70.68 - 88.35: 14 Dihedral angle restraints: 10299 sinusoidal: 4086 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 10296 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: 4.310 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 12.913 82.905 6240 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/Z covalent geometry : bond 0.00643 / 0.44 (17712) covalent geometry : angle 1.05667 / 0.69 (24030) SS BOND : bond 0.00757 / 0.59 ( 29) SS BOND : angle 9.07657 / 6.05 ( 58) hydrogen bonds : bond 0.24668 / 16.48 ( 630) hydrogen bonds : angle 8.45902 / 5.77 ( 1788) link_BETA1-4 : bond 0.00782 / 0.46 ( 12) link_BETA1-4 : angle 1.52386 / 1.05 ( 36) link_NAG-ASN : bond 0.00929 / 0.62 ( 24) link_NAG-ASN : angle 2.59840 / 1.79 ( 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 : 0.695 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: 0.1160 time to fit residues: 70.5750 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 : 0.684 ------------------------------------------------------------------------------- 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... A 48 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 50 ASN B 111 HIS C 60 GLN ** 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 = 0.3217 r_free = 0.3217 target = 0.066259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049938 restraints weight = 61367.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052037 restraints weight = 30847.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.053446 restraints weight = 20099.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054410 restraints weight = 15199.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055075 restraints weight = 12530.810| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17777 Z= 0.332 Angle : 0.757 10.390 24196 Z= 0.392 Chirality : 0.046 0.272 2721 Planarity : 0.005 0.045 3063 Dihedral : 4.997 41.549 2317 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 10.86 % Favored : 86.74 % 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: 0.31 (0.17), residues: 2139 helix: 2.16 (0.26), residues: 381 sheet: 0.82 (0.23), residues: 516 loop : -0.70 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 106 TYR 0.027 0.002 TYR L 49 PHE 0.025 0.002 PHE C 147 TRP 0.027 0.002 TRP E 153 HIS 0.010 0.002 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.33 (17712) covalent geometry : angle 0.74297 / 0.39 (24030) SS BOND : bond 0.00742 / 0.50 ( 29) SS BOND : angle 1.87279 / 1.30 ( 58) hydrogen bonds : bond 0.05356 / 3.67 ( 630) hydrogen bonds : angle 6.12879 / 4.23 ( 1788) link_BETA1-4 : bond 0.00279 / 0.17 ( 12) link_BETA1-4 : angle 1.49546 / 1.03 ( 36) link_NAG-ASN : bond 0.00720 / 0.43 ( 24) link_NAG-ASN : angle 2.03671 / 1.45 ( 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 314 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.697 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: 0.8548 (mp10) cc_final: 0.8239 (mp10) REVERT: L 32 TRP cc_start: 0.8709 (m-10) cc_final: 0.8188 (m-10) REVERT: H 39 GLN cc_start: 0.9276 (tt0) cc_final: 0.8845 (tt0) REVERT: H 60 ASN cc_start: 0.9281 (t0) cc_final: 0.8763 (t0) REVERT: H 72 ASP cc_start: 0.9006 (p0) cc_final: 0.8804 (p0) REVERT: H 105 GLN cc_start: 0.8944 (mm110) cc_final: 0.8642 (pp30) REVERT: A 14 CYS cc_start: 0.8700 (m) cc_final: 0.8028 (m) REVERT: A 53 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 105 TYR cc_start: 0.8634 (t80) cc_final: 0.8430 (t80) REVERT: A 225 ASP cc_start: 0.8249 (t70) cc_final: 0.7932 (t0) REVERT: B 112 ASP cc_start: 0.8756 (t0) cc_final: 0.8532 (t0) REVERT: C 24 ASP cc_start: 0.8408 (m-30) cc_final: 0.8115 (m-30) REVERT: D 77 MET cc_start: 0.8603 (mtt) cc_final: 0.8203 (mtt) REVERT: D 109 ASP cc_start: 0.9004 (t0) cc_final: 0.8685 (t0) REVERT: D 113 SER cc_start: 0.9597 (t) cc_final: 0.9223 (p) REVERT: E 24 ASP cc_start: 0.8663 (m-30) cc_final: 0.8222 (p0) REVERT: E 98 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7741 (m-10) REVERT: F 28 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7152 (t0) REVERT: F 101 LEU cc_start: 0.8957 (mp) cc_final: 0.8587 (mt) REVERT: F 141 TYR cc_start: 0.7921 (m-80) cc_final: 0.7388 (m-80) REVERT: J 47 LEU cc_start: 0.9303 (mp) cc_final: 0.8908 (mp) REVERT: G 77 GLN cc_start: 0.8218 (pp30) cc_final: 0.7525 (pp30) REVERT: K 4 MET cc_start: 0.8938 (mmm) cc_final: 0.8690 (mmm) REVERT: K 49 TYR cc_start: 0.9014 (p90) cc_final: 0.8813 (p90) outliers start: 45 outliers final: 22 residues processed: 303 average time/residue: 0.1138 time to fit residues: 55.2879 Evaluate side-chains 263 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 F residue 91 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 88 CYS 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: 2.9990 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS D 38 GLN E 158 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051071 restraints weight = 61027.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053256 restraints weight = 29974.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054721 restraints weight = 19230.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055722 restraints weight = 14352.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056363 restraints weight = 11731.994| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2550 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= 0.147 Angle : 0.605 10.644 24196 Z= 0.311 Chirality : 0.043 0.259 2721 Planarity : 0.004 0.041 3063 Dihedral : 4.448 22.356 2313 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.92 % Allowed : 13.68 % Favored : 84.40 % 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: 0.49 (0.18), residues: 2139 helix: 2.43 (0.27), residues: 375 sheet: 0.91 (0.23), residues: 522 loop : -0.61 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.022 0.001 TYR C 168 PHE 0.020 0.002 PHE I 78 TRP 0.020 0.001 TRP K 32 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17712) covalent geometry : angle 0.59436 / 0.31 (24030) SS BOND : bond 0.00389 / 0.22 ( 29) SS BOND : angle 1.55536 / 1.03 ( 58) hydrogen bonds : bond 0.04895 / 3.36 ( 630) hydrogen bonds : angle 5.61932 / 3.88 ( 1788) link_BETA1-4 : bond 0.00347 / 0.21 ( 12) link_BETA1-4 : angle 1.20672 / 0.82 ( 36) link_NAG-ASN : bond 0.00223 / 0.12 ( 24) link_NAG-ASN : angle 1.56609 / 1.11 ( 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 319 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.722 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: 0.8514 (mp10) cc_final: 0.7988 (mp10) REVERT: L 27 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8300 (mm-40) REVERT: L 32 TRP cc_start: 0.8673 (m-10) cc_final: 0.8135 (m-10) REVERT: L 98 PHE cc_start: 0.8331 (m-80) cc_final: 0.8124 (m-10) REVERT: H 39 GLN cc_start: 0.9280 (tt0) cc_final: 0.8501 (tm-30) REVERT: H 60 ASN cc_start: 0.9263 (t0) cc_final: 0.8757 (t0) REVERT: H 100 ILE cc_start: 0.8896 (tp) cc_final: 0.8609 (mp) REVERT: H 105 GLN cc_start: 0.8931 (mm110) cc_final: 0.8615 (pp30) REVERT: A 14 CYS cc_start: 0.8733 (m) cc_final: 0.8023 (m) REVERT: A 225 ASP cc_start: 0.8184 (t70) cc_final: 0.7846 (t0) REVERT: A 241 ASP cc_start: 0.6813 (t0) cc_final: 0.6469 (p0) REVERT: A 265 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8288 (t) REVERT: B 90 ASP cc_start: 0.8553 (m-30) cc_final: 0.8183 (m-30) REVERT: B 112 ASP cc_start: 0.8693 (t0) cc_final: 0.8487 (t0) REVERT: C 24 ASP cc_start: 0.8446 (m-30) cc_final: 0.8111 (m-30) REVERT: C 278 ASP cc_start: 0.8971 (t70) cc_final: 0.8771 (t70) REVERT: D 17 MET cc_start: 0.8905 (ttp) cc_final: 0.8478 (ppp) REVERT: D 77 MET cc_start: 0.8590 (mtt) cc_final: 0.8183 (mtt) REVERT: D 109 ASP cc_start: 0.8942 (t0) cc_final: 0.8597 (t0) REVERT: D 112 ASP cc_start: 0.8968 (m-30) cc_final: 0.8607 (t0) REVERT: D 113 SER cc_start: 0.9567 (t) cc_final: 0.9144 (p) REVERT: E 24 ASP cc_start: 0.8559 (m-30) cc_final: 0.8211 (p0) REVERT: E 98 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: E 152 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (pt) REVERT: F 101 LEU cc_start: 0.8864 (mp) cc_final: 0.8436 (mt) REVERT: F 113 SER cc_start: 0.9576 (t) cc_final: 0.9216 (p) REVERT: F 141 TYR cc_start: 0.7839 (m-80) cc_final: 0.7393 (m-80) REVERT: J 36 TYR cc_start: 0.8215 (m-80) cc_final: 0.7924 (m-10) REVERT: J 47 LEU cc_start: 0.9301 (mp) cc_final: 0.8958 (mp) REVERT: G 72 ASP cc_start: 0.7687 (m-30) cc_final: 0.6998 (m-30) REVERT: G 75 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8648 (mppt) REVERT: G 77 GLN cc_start: 0.8301 (pp30) cc_final: 0.7602 (pp30) REVERT: K 1 ASP cc_start: 0.8116 (t0) cc_final: 0.7916 (t0) REVERT: I 100 PHE cc_start: 0.9055 (m-80) cc_final: 0.8821 (m-80) outliers start: 36 outliers final: 17 residues processed: 306 average time/residue: 0.1138 time to fit residues: 56.2849 Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 152 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 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: 2.9990 chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** E 191 GLN ** 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 27 GLN 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 = 0.3139 r_free = 0.3139 target = 0.063441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.048085 restraints weight = 60797.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.050206 restraints weight = 29718.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051643 restraints weight = 19086.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.052617 restraints weight = 14265.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053282 restraints weight = 11671.301| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17777 Z= 0.193 Angle : 0.626 16.504 24196 Z= 0.318 Chirality : 0.044 0.255 2721 Planarity : 0.004 0.043 3063 Dihedral : 4.507 33.088 2313 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 14.75 % Favored : 82.85 % 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: 0.42 (0.18), residues: 2139 helix: 2.49 (0.27), residues: 375 sheet: 0.94 (0.24), residues: 495 loop : -0.70 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.017 0.001 TYR C 168 PHE 0.020 0.002 PHE I 78 TRP 0.019 0.001 TRP K 32 HIS 0.004 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17712) covalent geometry : angle 0.61459 / 0.32 (24030) SS BOND : bond 0.00526 / 0.39 ( 29) SS BOND : angle 1.71695 / 1.20 ( 58) hydrogen bonds : bond 0.04617 / 3.15 ( 630) hydrogen bonds : angle 5.40833 / 3.77 ( 1788) link_BETA1-4 : bond 0.00291 / 0.18 ( 12) link_BETA1-4 : angle 1.20005 / 0.82 ( 36) link_NAG-ASN : bond 0.00336 / 0.19 ( 24) link_NAG-ASN : angle 1.56473 / 1.08 ( 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 308 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8533 (mp10) cc_final: 0.8101 (mp10) REVERT: L 32 TRP cc_start: 0.8652 (m-10) cc_final: 0.8372 (m-10) REVERT: L 70 ASP cc_start: 0.9040 (t0) cc_final: 0.8793 (p0) REVERT: L 98 PHE cc_start: 0.8448 (m-80) cc_final: 0.8181 (m-10) REVERT: H 39 GLN cc_start: 0.9324 (tt0) cc_final: 0.8488 (tm-30) REVERT: H 60 ASN cc_start: 0.9265 (t0) cc_final: 0.8714 (t0) REVERT: H 100 ARG cc_start: 0.7654 (mmp80) cc_final: 0.7403 (mmp80) REVERT: H 105 GLN cc_start: 0.8988 (mm110) cc_final: 0.8608 (pp30) REVERT: A 14 CYS cc_start: 0.8774 (m) cc_final: 0.7990 (m) REVERT: A 241 ASP cc_start: 0.7290 (t0) cc_final: 0.6784 (p0) REVERT: A 265 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8093 (t) REVERT: B 90 ASP cc_start: 0.8715 (m-30) cc_final: 0.8345 (m-30) REVERT: B 149 MET cc_start: 0.9294 (mpp) cc_final: 0.8880 (mmt) REVERT: C 24 ASP cc_start: 0.8507 (m-30) cc_final: 0.8177 (m-30) REVERT: D 17 MET cc_start: 0.8938 (ttp) cc_final: 0.8653 (ppp) REVERT: D 59 MET cc_start: 0.9221 (tpp) cc_final: 0.8517 (tpp) REVERT: D 77 MET cc_start: 0.8585 (mtt) cc_final: 0.8165 (mtt) REVERT: D 109 ASP cc_start: 0.9134 (t0) cc_final: 0.8658 (t0) REVERT: D 112 ASP cc_start: 0.9136 (m-30) cc_final: 0.8672 (p0) REVERT: E 24 ASP cc_start: 0.8703 (m-30) cc_final: 0.8242 (p0) REVERT: E 98 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: F 101 LEU cc_start: 0.8848 (mp) cc_final: 0.8472 (mt) REVERT: F 113 SER cc_start: 0.9580 (t) cc_final: 0.9202 (p) REVERT: F 141 TYR cc_start: 0.8174 (m-80) cc_final: 0.7644 (m-80) REVERT: J 17 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.9023 (p0) REVERT: J 47 LEU cc_start: 0.9264 (mp) cc_final: 0.8841 (mp) REVERT: G 72 ASP cc_start: 0.7855 (m-30) cc_final: 0.7048 (m-30) REVERT: G 75 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8602 (mppt) REVERT: G 77 GLN cc_start: 0.8281 (pp30) cc_final: 0.7566 (pp30) REVERT: G 87 THR cc_start: 0.8981 (t) cc_final: 0.8657 (m) REVERT: G 97 ILE cc_start: 0.9382 (mm) cc_final: 0.9181 (tp) outliers start: 45 outliers final: 27 residues processed: 294 average time/residue: 0.1158 time to fit residues: 54.8984 Evaluate side-chains 271 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 53 LEU Chi-restraints excluded: chain A residue 113 SER 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 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 18 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 82 ASN 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 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: 0.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3161 r_free = 0.3161 target = 0.064402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.049075 restraints weight = 59896.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.051226 restraints weight = 29257.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.052708 restraints weight = 18716.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.053710 restraints weight = 13909.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054387 restraints weight = 11332.892| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17777 Z= 0.126 Angle : 0.587 9.866 24196 Z= 0.297 Chirality : 0.043 0.251 2721 Planarity : 0.004 0.052 3063 Dihedral : 4.211 22.577 2313 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 15.87 % Favored : 82.37 % 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: 0.48 (0.18), residues: 2139 helix: 2.51 (0.27), residues: 375 sheet: 0.99 (0.24), residues: 495 loop : -0.67 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 24 TYR 0.013 0.001 TYR L 49 PHE 0.017 0.001 PHE I 78 TRP 0.015 0.001 TRP K 32 HIS 0.002 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17712) covalent geometry : angle 0.57653 / 0.29 (24030) SS BOND : bond 0.00437 / 0.30 ( 29) SS BOND : angle 1.61952 / 1.00 ( 58) hydrogen bonds : bond 0.04415 / 3.04 ( 630) hydrogen bonds : angle 5.11621 / 3.58 ( 1788) link_BETA1-4 : bond 0.00352 / 0.22 ( 12) link_BETA1-4 : angle 1.14835 / 0.79 ( 36) link_NAG-ASN : bond 0.00174 / 0.10 ( 24) link_NAG-ASN : angle 1.46808 / 1.01 ( 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 305 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8508 (mp10) cc_final: 0.7930 (mp10) REVERT: L 27 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8294 (mm-40) REVERT: L 32 TRP cc_start: 0.8613 (m-10) cc_final: 0.8371 (m-10) REVERT: L 70 ASP cc_start: 0.9019 (t0) cc_final: 0.8785 (p0) REVERT: L 82 ASP cc_start: 0.8303 (m-30) cc_final: 0.7965 (m-30) REVERT: H 39 GLN cc_start: 0.9303 (tt0) cc_final: 0.8528 (tm-30) REVERT: H 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8755 (t0) REVERT: H 100 ILE cc_start: 0.8848 (tp) cc_final: 0.8550 (mp) REVERT: H 100 ARG cc_start: 0.7717 (mmp80) cc_final: 0.7384 (mmp80) REVERT: A 14 CYS cc_start: 0.8772 (m) cc_final: 0.7986 (m) REVERT: A 241 ASP cc_start: 0.7290 (t0) cc_final: 0.6883 (p0) REVERT: A 265 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 90 ASP cc_start: 0.8720 (m-30) cc_final: 0.8309 (m-30) REVERT: C 24 ASP cc_start: 0.8527 (m-30) cc_final: 0.8204 (m-30) REVERT: D 17 MET cc_start: 0.8866 (ttp) cc_final: 0.8651 (ppp) REVERT: D 77 MET cc_start: 0.8569 (mtt) cc_final: 0.8135 (mtt) REVERT: D 97 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: D 109 ASP cc_start: 0.9107 (t0) cc_final: 0.8625 (t0) REVERT: D 112 ASP cc_start: 0.9097 (m-30) cc_final: 0.8720 (p0) REVERT: D 113 SER cc_start: 0.9564 (t) cc_final: 0.8830 (p) REVERT: D 140 PHE cc_start: 0.8612 (m-80) cc_final: 0.8310 (m-80) REVERT: E 24 ASP cc_start: 0.8671 (m-30) cc_final: 0.8270 (p0) REVERT: E 98 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: F 17 MET cc_start: 0.7812 (ttp) cc_final: 0.7131 (ttp) REVERT: F 101 LEU cc_start: 0.8815 (mp) cc_final: 0.8482 (mt) REVERT: F 113 SER cc_start: 0.9575 (t) cc_final: 0.9210 (p) REVERT: F 141 TYR cc_start: 0.8109 (m-80) cc_final: 0.7600 (m-80) REVERT: J 27 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8584 (tp40) REVERT: J 47 LEU cc_start: 0.9253 (mp) cc_final: 0.8840 (mp) REVERT: G 46 GLU cc_start: 0.7384 (mp0) cc_final: 0.7023 (mp0) REVERT: G 72 ASP cc_start: 0.7839 (m-30) cc_final: 0.7035 (m-30) REVERT: G 75 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8586 (mppt) REVERT: G 77 GLN cc_start: 0.8300 (pp30) cc_final: 0.7550 (pp30) REVERT: G 87 THR cc_start: 0.8940 (t) cc_final: 0.8627 (m) REVERT: K 1 ASP cc_start: 0.8295 (t0) cc_final: 0.8048 (t0) REVERT: K 27 GLN cc_start: 0.8349 (mt0) cc_final: 0.8119 (pt0) REVERT: I 100 PHE cc_start: 0.9188 (m-80) cc_final: 0.8967 (m-80) outliers start: 33 outliers final: 20 residues processed: 292 average time/residue: 0.1149 time to fit residues: 53.8848 Evaluate side-chains 267 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 D residue 97 GLU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN ** E 191 GLN ** 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 = 0.3150 r_free = 0.3150 target = 0.063941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.048663 restraints weight = 59909.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.050776 restraints weight = 29367.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052222 restraints weight = 18889.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.053194 restraints weight = 14084.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053876 restraints weight = 11527.722| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17777 Z= 0.159 Angle : 0.606 11.800 24196 Z= 0.306 Chirality : 0.043 0.251 2721 Planarity : 0.004 0.055 3063 Dihedral : 4.271 26.802 2313 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.24 % Allowed : 16.03 % Favored : 81.74 % Cbeta Deviations : 0.05 % 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: 0.45 (0.18), residues: 2139 helix: 2.55 (0.27), residues: 372 sheet: 0.89 (0.24), residues: 501 loop : -0.66 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100F TYR 0.012 0.001 TYR L 49 PHE 0.016 0.001 PHE I 78 TRP 0.015 0.001 TRP K 32 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (17712) covalent geometry : angle 0.59282 / 0.30 (24030) SS BOND : bond 0.00383 / 0.24 ( 29) SS BOND : angle 1.97149 / 1.10 ( 58) hydrogen bonds : bond 0.04373 / 3.00 ( 630) hydrogen bonds : angle 5.13270 / 3.61 ( 1788) link_BETA1-4 : bond 0.00320 / 0.20 ( 12) link_BETA1-4 : angle 1.15379 / 0.79 ( 36) link_NAG-ASN : bond 0.00231 / 0.13 ( 24) link_NAG-ASN : angle 1.50005 / 1.03 ( 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 299 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8498 (mp10) cc_final: 0.7916 (mp10) REVERT: L 27 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8316 (mm-40) REVERT: L 32 TRP cc_start: 0.8641 (m-10) cc_final: 0.8416 (m-10) REVERT: L 70 ASP cc_start: 0.9050 (t0) cc_final: 0.8819 (p0) REVERT: L 82 ASP cc_start: 0.8345 (m-30) cc_final: 0.8007 (m-30) REVERT: H 39 GLN cc_start: 0.9313 (tt0) cc_final: 0.8521 (tm-30) REVERT: H 60 ASN cc_start: 0.9281 (t0) cc_final: 0.8762 (t0) REVERT: H 100 ARG cc_start: 0.7592 (mmp80) cc_final: 0.7339 (mmp80) REVERT: A 14 CYS cc_start: 0.8760 (m) cc_final: 0.7991 (m) REVERT: A 241 ASP cc_start: 0.7453 (t0) cc_final: 0.7018 (p0) REVERT: A 265 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7954 (t) REVERT: B 149 MET cc_start: 0.9200 (mmt) cc_final: 0.8935 (mmt) REVERT: C 24 ASP cc_start: 0.8533 (m-30) cc_final: 0.8211 (m-30) REVERT: D 17 MET cc_start: 0.8906 (ttp) cc_final: 0.8683 (ppp) REVERT: D 58 LYS cc_start: 0.9496 (mmmt) cc_final: 0.9191 (mmmm) REVERT: D 59 MET cc_start: 0.9217 (tpp) cc_final: 0.8346 (tpp) REVERT: D 77 MET cc_start: 0.8584 (mtt) cc_final: 0.8126 (mtt) REVERT: D 109 ASP cc_start: 0.9084 (t0) cc_final: 0.8636 (t0) REVERT: D 112 ASP cc_start: 0.9117 (m-30) cc_final: 0.8735 (p0) REVERT: D 113 SER cc_start: 0.9573 (t) cc_final: 0.8829 (p) REVERT: D 140 PHE cc_start: 0.8772 (m-80) cc_final: 0.8400 (m-80) REVERT: E 24 ASP cc_start: 0.8678 (m-30) cc_final: 0.8306 (p0) REVERT: E 98 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: F 17 MET cc_start: 0.7884 (ttp) cc_final: 0.7155 (ttp) REVERT: F 105 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8581 (mm-30) REVERT: F 113 SER cc_start: 0.9582 (t) cc_final: 0.9206 (p) REVERT: F 141 TYR cc_start: 0.8171 (m-80) cc_final: 0.7632 (m-80) REVERT: J 27 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8626 (tp40) REVERT: J 47 LEU cc_start: 0.9229 (mp) cc_final: 0.8863 (mp) REVERT: G 46 GLU cc_start: 0.7415 (mp0) cc_final: 0.7053 (mp0) REVERT: G 72 ASP cc_start: 0.7951 (m-30) cc_final: 0.7180 (m-30) REVERT: G 75 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8583 (mppt) REVERT: G 77 GLN cc_start: 0.8287 (pp30) cc_final: 0.7635 (pp30) REVERT: G 87 THR cc_start: 0.8938 (t) cc_final: 0.8632 (m) REVERT: K 27 GLN cc_start: 0.8378 (mt0) cc_final: 0.8159 (pt0) REVERT: I 100 PHE cc_start: 0.9189 (m-80) cc_final: 0.8989 (m-80) outliers start: 42 outliers final: 24 residues processed: 285 average time/residue: 0.1131 time to fit residues: 51.9176 Evaluate side-chains 267 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain A residue 113 SER 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 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 E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 10 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048888 restraints weight = 59820.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051017 restraints weight = 29382.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.052480 restraints weight = 18859.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053466 restraints weight = 14061.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054108 restraints weight = 11488.092| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17777 Z= 0.135 Angle : 0.600 11.458 24196 Z= 0.301 Chirality : 0.043 0.250 2721 Planarity : 0.004 0.056 3063 Dihedral : 4.195 20.209 2313 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.76 % Allowed : 17.09 % Favored : 81.15 % 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: 0.49 (0.18), residues: 2139 helix: 2.52 (0.27), residues: 375 sheet: 0.90 (0.24), residues: 501 loop : -0.61 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.011 0.001 TYR L 49 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/Z covalent geometry : bond 0.00308 / 0.13 (17712) covalent geometry : angle 0.59019 / 0.30 (24030) SS BOND : bond 0.00431 / 0.31 ( 29) SS BOND : angle 1.55993 / 0.93 ( 58) hydrogen bonds : bond 0.04285 / 2.95 ( 630) hydrogen bonds : angle 5.03507 / 3.55 ( 1788) link_BETA1-4 : bond 0.00328 / 0.20 ( 12) link_BETA1-4 : angle 1.13966 / 0.78 ( 36) link_NAG-ASN : bond 0.00178 / 0.10 ( 24) link_NAG-ASN : angle 1.47405 / 1.01 ( 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 291 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8482 (mp10) cc_final: 0.7887 (mp10) REVERT: L 27 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8426 (mm-40) REVERT: L 32 TRP cc_start: 0.8599 (m-10) cc_final: 0.8244 (m-10) REVERT: L 70 ASP cc_start: 0.9034 (t0) cc_final: 0.8825 (p0) REVERT: L 78 LEU cc_start: 0.9019 (tt) cc_final: 0.8672 (tt) REVERT: L 82 ASP cc_start: 0.8357 (m-30) cc_final: 0.7996 (m-30) REVERT: L 98 PHE cc_start: 0.8074 (m-80) cc_final: 0.7788 (m-10) REVERT: H 60 ASN cc_start: 0.9282 (t0) cc_final: 0.8755 (t0) REVERT: H 100 ILE cc_start: 0.8886 (tp) cc_final: 0.8549 (mp) REVERT: A 14 CYS cc_start: 0.8745 (m) cc_final: 0.7975 (m) REVERT: A 241 ASP cc_start: 0.7417 (t0) cc_final: 0.7062 (p0) REVERT: A 265 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7883 (t) REVERT: A 305 CYS cc_start: 0.5668 (p) cc_final: 0.5402 (p) REVERT: B 149 MET cc_start: 0.9218 (mmt) cc_final: 0.8973 (mmm) REVERT: C 24 ASP cc_start: 0.8544 (m-30) cc_final: 0.8235 (m-30) REVERT: D 17 MET cc_start: 0.8903 (ttp) cc_final: 0.8691 (ppp) REVERT: D 58 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9225 (mmmm) REVERT: D 59 MET cc_start: 0.9219 (tpp) cc_final: 0.8364 (tpp) REVERT: D 77 MET cc_start: 0.8590 (mtt) cc_final: 0.8119 (mtt) REVERT: D 97 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: D 109 ASP cc_start: 0.9071 (t0) cc_final: 0.8608 (t0) REVERT: D 112 ASP cc_start: 0.9105 (m-30) cc_final: 0.8742 (p0) REVERT: D 113 SER cc_start: 0.9566 (t) cc_final: 0.8824 (p) REVERT: D 140 PHE cc_start: 0.8744 (m-80) cc_final: 0.8391 (m-80) REVERT: E 24 ASP cc_start: 0.8706 (m-30) cc_final: 0.8362 (p0) REVERT: E 98 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: F 17 MET cc_start: 0.7863 (ttp) cc_final: 0.6967 (ttp) REVERT: F 105 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8536 (mm-30) REVERT: F 113 SER cc_start: 0.9586 (t) cc_final: 0.9212 (p) REVERT: F 141 TYR cc_start: 0.8180 (m-80) cc_final: 0.7655 (m-80) REVERT: J 27 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8668 (tp40) REVERT: J 42 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8540 (mmmm) REVERT: J 47 LEU cc_start: 0.9226 (mp) cc_final: 0.8819 (mp) REVERT: G 5 GLN cc_start: 0.8307 (tm130) cc_final: 0.8067 (tm-30) REVERT: G 46 GLU cc_start: 0.7425 (mp0) cc_final: 0.7075 (mp0) REVERT: G 72 ASP cc_start: 0.7930 (m-30) cc_final: 0.7128 (m-30) REVERT: G 75 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8598 (mppt) REVERT: G 77 GLN cc_start: 0.8318 (pp30) cc_final: 0.7640 (pp30) REVERT: G 87 THR cc_start: 0.8909 (t) cc_final: 0.8599 (m) REVERT: K 1 ASP cc_start: 0.8304 (t0) cc_final: 0.8033 (t0) REVERT: K 27 GLN cc_start: 0.8444 (mt0) cc_final: 0.8202 (pt0) REVERT: I 95 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6711 (mm-30) outliers start: 33 outliers final: 23 residues processed: 279 average time/residue: 0.1138 time to fit residues: 50.6084 Evaluate side-chains 271 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 H residue 100 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 113 SER 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 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 G residue 24 VAL Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain K residue 46 LEU 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: 5.9990 chunk 134 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** E 191 GLN ** 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 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.048795 restraints weight = 60133.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.050921 restraints weight = 29567.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052385 restraints weight = 18994.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.053371 restraints weight = 14171.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054050 restraints weight = 11566.947| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17777 Z= 0.142 Angle : 0.629 12.101 24196 Z= 0.315 Chirality : 0.043 0.249 2721 Planarity : 0.004 0.056 3063 Dihedral : 4.350 32.382 2313 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.65 % Allowed : 17.47 % Favored : 80.88 % Cbeta Deviations : 0.05 % 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: 0.49 (0.18), residues: 2139 helix: 2.50 (0.27), residues: 375 sheet: 0.92 (0.24), residues: 495 loop : -0.62 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 100F TYR 0.018 0.001 TYR H 58 PHE 0.026 0.001 PHE J 98 TRP 0.017 0.001 TRP I 103 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17712) covalent geometry : angle 0.61347 / 0.31 (24030) SS BOND : bond 0.00336 / 0.22 ( 29) SS BOND : angle 2.32954 / 1.35 ( 58) hydrogen bonds : bond 0.04274 / 2.96 ( 630) hydrogen bonds : angle 5.08141 / 3.59 ( 1788) link_BETA1-4 : bond 0.00340 / 0.21 ( 12) link_BETA1-4 : angle 1.14004 / 0.78 ( 36) link_NAG-ASN : bond 0.00186 / 0.10 ( 24) link_NAG-ASN : angle 1.47265 / 1.01 ( 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 291 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8474 (mp10) cc_final: 0.7875 (mp10) REVERT: L 27 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8478 (mm-40) REVERT: L 78 LEU cc_start: 0.9014 (tt) cc_final: 0.8669 (tt) REVERT: L 82 ASP cc_start: 0.8384 (m-30) cc_final: 0.8008 (m-30) REVERT: L 98 PHE cc_start: 0.8185 (m-80) cc_final: 0.7856 (m-10) REVERT: H 60 ASN cc_start: 0.9263 (t0) cc_final: 0.8728 (t0) REVERT: H 100 ILE cc_start: 0.8911 (tp) cc_final: 0.8683 (mp) REVERT: A 14 CYS cc_start: 0.8742 (m) cc_final: 0.7977 (m) REVERT: A 241 ASP cc_start: 0.7435 (t70) cc_final: 0.7129 (p0) REVERT: A 265 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7891 (t) REVERT: A 305 CYS cc_start: 0.5711 (p) cc_final: 0.5474 (p) REVERT: B 90 ASP cc_start: 0.8838 (m-30) cc_final: 0.8580 (m-30) REVERT: B 149 MET cc_start: 0.9230 (mmt) cc_final: 0.9000 (mmm) REVERT: C 24 ASP cc_start: 0.8553 (m-30) cc_final: 0.8239 (m-30) REVERT: D 17 MET cc_start: 0.8918 (ttp) cc_final: 0.8701 (ppp) REVERT: D 58 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9251 (mmmm) REVERT: D 97 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: D 106 ARG cc_start: 0.9215 (ttm-80) cc_final: 0.8973 (ttm-80) REVERT: D 109 ASP cc_start: 0.9040 (t0) cc_final: 0.8558 (t0) REVERT: D 112 ASP cc_start: 0.9118 (m-30) cc_final: 0.8682 (p0) REVERT: D 113 SER cc_start: 0.9565 (t) cc_final: 0.8813 (p) REVERT: D 140 PHE cc_start: 0.8748 (m-80) cc_final: 0.8392 (m-80) REVERT: E 24 ASP cc_start: 0.8706 (m-30) cc_final: 0.8358 (p0) REVERT: E 98 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: F 17 MET cc_start: 0.7713 (ttp) cc_final: 0.6811 (ttp) REVERT: F 53 ASN cc_start: 0.9027 (m-40) cc_final: 0.8803 (m-40) REVERT: F 105 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8525 (mm-30) REVERT: F 141 TYR cc_start: 0.8203 (m-80) cc_final: 0.7688 (m-80) REVERT: J 27 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8686 (tp40) REVERT: J 42 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8581 (mmmm) REVERT: J 47 LEU cc_start: 0.9150 (mp) cc_final: 0.8820 (mp) REVERT: G 3 GLN cc_start: 0.8272 (mm110) cc_final: 0.8027 (mm-40) REVERT: G 5 GLN cc_start: 0.8314 (tm130) cc_final: 0.8002 (tm-30) REVERT: G 46 GLU cc_start: 0.7417 (mp0) cc_final: 0.7068 (mp0) REVERT: G 72 ASP cc_start: 0.7944 (m-30) cc_final: 0.7140 (m-30) REVERT: G 75 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8599 (mppt) REVERT: G 77 GLN cc_start: 0.8341 (pp30) cc_final: 0.7647 (pp30) REVERT: G 87 THR cc_start: 0.8902 (t) cc_final: 0.8587 (m) REVERT: K 27 GLN cc_start: 0.8471 (mt0) cc_final: 0.8246 (pt0) REVERT: I 3 GLN cc_start: 0.8139 (mm110) cc_final: 0.7843 (mm-40) outliers start: 31 outliers final: 24 residues processed: 281 average time/residue: 0.1155 time to fit residues: 51.8616 Evaluate side-chains 276 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU 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 88 VAL Chi-restraints excluded: chain A residue 113 SER 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 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 104 ASP Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain G residue 24 VAL 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 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: 7.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 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: 0.0270 chunk 203 optimal weight: 5.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** E 191 GLN ** 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.046205 restraints weight = 61755.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048222 restraints weight = 31112.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049610 restraints weight = 20375.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.050561 restraints weight = 15417.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051162 restraints weight = 12708.977| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17777 Z= 0.264 Angle : 0.692 12.482 24196 Z= 0.351 Chirality : 0.044 0.251 2721 Planarity : 0.004 0.059 3063 Dihedral : 4.526 26.175 2313 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 17.78 % Favored : 80.62 % 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: 0.24 (0.18), residues: 2139 helix: 2.18 (0.27), residues: 375 sheet: 0.60 (0.24), residues: 501 loop : -0.66 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 100F TYR 0.022 0.002 TYR D 119 PHE 0.028 0.002 PHE J 98 TRP 0.023 0.002 TRP K 32 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (17712) covalent geometry : angle 0.68125 / 0.35 (24030) SS BOND : bond 0.00518 / 0.35 ( 29) SS BOND : angle 1.71356 / 1.04 ( 58) hydrogen bonds : bond 0.04558 / 3.15 ( 630) hydrogen bonds : angle 5.20533 / 3.65 ( 1788) link_BETA1-4 : bond 0.00265 / 0.15 ( 12) link_BETA1-4 : angle 1.22688 / 0.84 ( 36) link_NAG-ASN : bond 0.00510 / 0.28 ( 24) link_NAG-ASN : angle 1.76400 / 1.20 ( 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 273 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8440 (mp10) cc_final: 0.7994 (mp10) REVERT: L 32 TRP cc_start: 0.8673 (m-10) cc_final: 0.8314 (m-10) REVERT: L 78 LEU cc_start: 0.9085 (tt) cc_final: 0.8810 (tt) REVERT: H 33 CYS cc_start: 0.7594 (m) cc_final: 0.7253 (m) REVERT: H 56 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.7876 (t) REVERT: H 60 ASN cc_start: 0.9312 (t0) cc_final: 0.8826 (t0) REVERT: A 14 CYS cc_start: 0.8745 (m) cc_final: 0.8013 (m) REVERT: A 225 ASP cc_start: 0.8213 (t0) cc_final: 0.7977 (t0) REVERT: A 265 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8136 (t) REVERT: A 305 CYS cc_start: 0.5615 (p) cc_final: 0.5378 (p) REVERT: B 149 MET cc_start: 0.9220 (mmt) cc_final: 0.8988 (mmm) REVERT: C 24 ASP cc_start: 0.8526 (m-30) cc_final: 0.8227 (m-30) REVERT: D 17 MET cc_start: 0.9005 (ttp) cc_final: 0.8776 (ppp) REVERT: D 106 ARG cc_start: 0.9186 (ttm-80) cc_final: 0.8939 (ttm-80) REVERT: D 109 ASP cc_start: 0.9026 (t0) cc_final: 0.8733 (t0) REVERT: D 112 ASP cc_start: 0.9116 (m-30) cc_final: 0.8651 (t0) REVERT: E 24 ASP cc_start: 0.8635 (m-30) cc_final: 0.8349 (p0) REVERT: E 98 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: F 17 MET cc_start: 0.8134 (ttp) cc_final: 0.7160 (ttp) REVERT: F 105 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8490 (mm-30) REVERT: F 141 TYR cc_start: 0.8364 (m-80) cc_final: 0.7800 (m-80) REVERT: J 27 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8806 (tp40) REVERT: J 47 LEU cc_start: 0.9281 (mp) cc_final: 0.8863 (mp) REVERT: G 5 GLN cc_start: 0.8321 (tm130) cc_final: 0.8082 (tm-30) REVERT: G 46 GLU cc_start: 0.7629 (mp0) cc_final: 0.7315 (mp0) REVERT: G 72 ASP cc_start: 0.8052 (m-30) cc_final: 0.7697 (m-30) REVERT: G 77 GLN cc_start: 0.8435 (pp30) cc_final: 0.7821 (pp30) REVERT: G 87 THR cc_start: 0.8932 (t) cc_final: 0.8651 (m) REVERT: K 27 GLN cc_start: 0.8532 (mt0) cc_final: 0.8276 (pt0) REVERT: I 3 GLN cc_start: 0.8237 (mm110) cc_final: 0.7952 (mm-40) outliers start: 30 outliers final: 25 residues processed: 265 average time/residue: 0.1218 time to fit residues: 51.6218 Evaluate side-chains 254 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE 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 113 SER 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 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 E residue 98 TYR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain G residue 24 VAL 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 I residue 5 GLN Chi-restraints excluded: chain I residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 177 optimal weight: 0.0970 chunk 179 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** E 191 GLN ** 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 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.047916 restraints weight = 59899.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.050014 restraints weight = 29768.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.051454 restraints weight = 19261.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052374 restraints weight = 14439.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053053 restraints weight = 11915.712| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17777 Z= 0.138 Angle : 0.652 12.877 24196 Z= 0.326 Chirality : 0.044 0.246 2721 Planarity : 0.004 0.057 3063 Dihedral : 4.380 25.619 2313 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.49 % Allowed : 18.32 % Favored : 80.19 % 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: 0.36 (0.18), residues: 2139 helix: 2.30 (0.27), residues: 381 sheet: 0.69 (0.24), residues: 501 loop : -0.62 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 100F TYR 0.018 0.001 TYR D 119 PHE 0.017 0.001 PHE J 98 TRP 0.011 0.001 TRP K 32 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17712) covalent geometry : angle 0.63856 / 0.32 (24030) SS BOND : bond 0.00363 / 0.25 ( 29) SS BOND : angle 2.21182 / 1.24 ( 58) hydrogen bonds : bond 0.04355 / 3.01 ( 630) hydrogen bonds : angle 5.13476 / 3.63 ( 1788) link_BETA1-4 : bond 0.00299 / 0.20 ( 12) link_BETA1-4 : angle 1.11122 / 0.76 ( 36) link_NAG-ASN : bond 0.00182 / 0.10 ( 24) link_NAG-ASN : angle 1.50338 / 1.02 ( 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 287 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8402 (mp10) cc_final: 0.7914 (mp10) REVERT: L 27 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8291 (mm-40) REVERT: L 78 LEU cc_start: 0.9143 (tt) cc_final: 0.8864 (tt) REVERT: H 33 CYS cc_start: 0.7306 (m) cc_final: 0.7103 (m) REVERT: H 56 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.7904 (t) REVERT: H 60 ASN cc_start: 0.9294 (t0) cc_final: 0.8754 (t0) REVERT: H 100 ILE cc_start: 0.8996 (tp) cc_final: 0.8744 (mp) REVERT: A 14 CYS cc_start: 0.8804 (m) cc_final: 0.8036 (m) REVERT: A 225 ASP cc_start: 0.8229 (t0) cc_final: 0.7981 (t0) REVERT: A 241 ASP cc_start: 0.7581 (t0) cc_final: 0.7353 (p0) REVERT: A 265 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7704 (t) REVERT: B 90 ASP cc_start: 0.8857 (m-30) cc_final: 0.8584 (m-30) REVERT: B 106 ARG cc_start: 0.9504 (mmm-85) cc_final: 0.9236 (tpp80) REVERT: B 149 MET cc_start: 0.9253 (mmt) cc_final: 0.9039 (mmm) REVERT: B 168 LEU cc_start: 0.9815 (OUTLIER) cc_final: 0.9550 (pp) REVERT: C 24 ASP cc_start: 0.8569 (m-30) cc_final: 0.8255 (m-30) REVERT: D 97 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: D 106 ARG cc_start: 0.9246 (ttm-80) cc_final: 0.8697 (ttm-80) REVERT: D 109 ASP cc_start: 0.9043 (t0) cc_final: 0.8610 (t0) REVERT: D 112 ASP cc_start: 0.9131 (m-30) cc_final: 0.8730 (p0) REVERT: D 113 SER cc_start: 0.9575 (t) cc_final: 0.8833 (p) REVERT: D 140 PHE cc_start: 0.8806 (m-80) cc_final: 0.8458 (m-80) REVERT: E 24 ASP cc_start: 0.8682 (m-30) cc_final: 0.8338 (p0) REVERT: E 98 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: F 17 MET cc_start: 0.7926 (ttp) cc_final: 0.6925 (ttp) REVERT: F 42 GLN cc_start: 0.8876 (tt0) cc_final: 0.8458 (tt0) REVERT: F 53 ASN cc_start: 0.8990 (m-40) cc_final: 0.8777 (m-40) REVERT: F 58 LYS cc_start: 0.9369 (tppt) cc_final: 0.9066 (tppt) REVERT: F 105 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8480 (mm-30) REVERT: F 113 SER cc_start: 0.9580 (t) cc_final: 0.9208 (p) REVERT: F 141 TYR cc_start: 0.8333 (m-80) cc_final: 0.7782 (m-80) REVERT: J 27 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8756 (tp40) REVERT: J 47 LEU cc_start: 0.9159 (mp) cc_final: 0.8811 (mp) REVERT: G 5 GLN cc_start: 0.8341 (tm130) cc_final: 0.8116 (tm-30) REVERT: G 46 GLU cc_start: 0.7546 (mp0) cc_final: 0.7216 (mp0) REVERT: G 72 ASP cc_start: 0.8044 (m-30) cc_final: 0.7291 (m-30) REVERT: G 75 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8781 (mppt) REVERT: G 77 GLN cc_start: 0.8414 (pp30) cc_final: 0.7775 (pp30) REVERT: G 87 THR cc_start: 0.8891 (t) cc_final: 0.8593 (m) REVERT: G 100 ILE cc_start: 0.9274 (mm) cc_final: 0.8962 (mp) REVERT: G 105 GLN cc_start: 0.8524 (mt0) cc_final: 0.8242 (mp10) REVERT: K 27 GLN cc_start: 0.8550 (mt0) cc_final: 0.8266 (pt0) REVERT: I 3 GLN cc_start: 0.8210 (mm110) cc_final: 0.7913 (mm-40) outliers start: 28 outliers final: 20 residues processed: 279 average time/residue: 0.1188 time to fit residues: 52.8553 Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL 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 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 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 G residue 24 VAL 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 I residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.047818 restraints weight = 60069.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.049892 restraints weight = 29919.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.051305 restraints weight = 19392.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052218 restraints weight = 14549.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052868 restraints weight = 12002.707| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3848 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= 0.155 Angle : 0.664 12.986 24196 Z= 0.332 Chirality : 0.044 0.246 2721 Planarity : 0.004 0.058 3063 Dihedral : 4.439 27.271 2313 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.65 % Allowed : 18.48 % 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: 0.37 (0.18), residues: 2139 helix: 2.28 (0.27), residues: 381 sheet: 0.61 (0.24), residues: 522 loop : -0.58 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 262 TYR 0.019 0.001 TYR D 119 PHE 0.021 0.002 PHE L 98 TRP 0.012 0.001 TRP K 32 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17712) covalent geometry : angle 0.64778 / 0.33 (24030) SS BOND : bond 0.00404 / 0.27 ( 29) SS BOND : angle 2.51480 / 1.49 ( 58) hydrogen bonds : bond 0.04346 / 2.99 ( 630) hydrogen bonds : angle 5.13572 / 3.63 ( 1788) link_BETA1-4 : bond 0.00311 / 0.19 ( 12) link_BETA1-4 : angle 1.14154 / 0.78 ( 36) link_NAG-ASN : bond 0.00230 / 0.12 ( 24) link_NAG-ASN : angle 1.52098 / 1.03 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.65 seconds wall clock time: 47 minutes 6.46 seconds (2826.46 seconds total)