Starting phenix.real_space_refine on Mon Sep 14 20:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792.map" model { file = "/net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mem_23792/09_2026/7mem_23792_trim.cif" } resolution = 3.2 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= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 10602 2.51 5 N 2859 2.21 5 O 3318 1.98 5 H 16044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 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: 32898 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "D" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "C" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "J" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "F" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "K" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.49, per 1000 atoms: 0.17 Number of scatterers: 32898 At special positions: 0 Unit cell: (138.02, 140.08, 152.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3318 8.00 N 2859 7.00 C 10602 6.00 H 16044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS A 137 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.05 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 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 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 D 137 " - pdb=" SG CYS F 14 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS B 137 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.05 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 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 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 A 144 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 277 " distance=2.05 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 76 " distance=2.02 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 305 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG M 1 " - " FUC M 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG Q 1 " - " FUC Q 2 " NAG-ASN " NAG C 401 " - " ASN C 278 " " NAG C 402 " - " ASN C 289 " " NAG E 401 " - " ASN E 278 " " NAG E 402 " - " ASN E 289 " " NAG F 401 " - " ASN F 278 " " NAG F 402 " - " ASN F 289 " " NAG M 1 " - " ASN E 33 " " NAG N 1 " - " ASN E 94 " " NAG O 1 " - " ASN C 33 " " NAG P 1 " - " ASN C 94 " " NAG Q 1 " - " ASN F 33 " " NAG R 1 " - " ASN F 94 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 925.0 milliseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 51 sheets defined 20.6% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 159 through 169 removed outlier: 4.461A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 74 through 127 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 159 through 169 removed outlier: 4.462A pdb=" N GLU A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 72 Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' and resid 187 through 195 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 159 through 169 removed outlier: 4.461A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 6.533A pdb=" N CYS A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU E 51 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.339A pdb=" N ALA E 138 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.192A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 31 through 36 removed outlier: 6.533A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 65 removed outlier: 4.191A pdb=" N CYS F 281 " --> pdb=" O ILE F 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.534A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.338A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.191A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET G 34 " --> pdb=" O MET G 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AE3, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AE4, first strand: chain 'F' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU F 51 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS F 277 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU F 59 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 87 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 179 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 136 through 141 removed outlier: 7.339A pdb=" N ALA F 138 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA F 144 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 164 through 169 Processing sheet with id=AF1, first strand: chain 'K' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR K 97 " --> pdb=" O HIS K 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 1980 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: 8.11 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 755 1.00 - 1.23: 16007 1.23 - 1.45: 8058 1.45 - 1.67: 8363 1.67 - 1.90: 102 Bond restraints: 33285 Sorted by residual: bond pdb=" NE2 HIS K 32 " pdb=" HE2 HIS K 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" NE2 HIS J 32 " pdb=" HE2 HIS J 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" NE2 HIS L 32 " pdb=" HE2 HIS L 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" NE ARG C 224 " pdb=" HE ARG C 224 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" NE ARG E 224 " pdb=" HE ARG E 224 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.04e+01 ... (remaining 33280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 51030 2.60 - 5.20: 6067 5.20 - 7.80: 2403 7.80 - 10.40: 290 10.40 - 13.00: 21 Bond angle restraints: 59811 Sorted by residual: angle pdb=" CA ASP I 96 " pdb=" CB ASP I 96 " pdb=" CG ASP I 96 " ideal model delta sigma weight residual 112.60 104.66 7.94 1.00e+00 1.00e+00 6.31e+01 angle pdb=" CA ASP H 96 " pdb=" CB ASP H 96 " pdb=" CG ASP H 96 " ideal model delta sigma weight residual 112.60 104.68 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" CA ASP G 96 " pdb=" CB ASP G 96 " pdb=" CG ASP G 96 " ideal model delta sigma weight residual 112.60 104.70 7.90 1.00e+00 1.00e+00 6.24e+01 angle pdb=" C HIS F 184 " pdb=" N PRO F 185 " pdb=" CA PRO F 185 " ideal model delta sigma weight residual 119.78 127.85 -8.07 1.03e+00 9.43e-01 6.14e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.78 127.83 -8.05 1.03e+00 9.43e-01 6.11e+01 ... (remaining 59806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 15318 17.53 - 35.05: 486 35.05 - 52.58: 198 52.58 - 70.11: 99 70.11 - 87.64: 18 Dihedral angle restraints: 16119 sinusoidal: 8802 harmonic: 7317 Sorted by residual: dihedral pdb=" CA SER C 265 " pdb=" C SER C 265 " pdb=" N GLY C 266 " pdb=" CA GLY C 266 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA SER F 265 " pdb=" C SER F 265 " pdb=" N GLY F 266 " pdb=" CA GLY F 266 " ideal model delta harmonic sigma weight residual 180.00 -146.03 -33.97 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA SER E 265 " pdb=" C SER E 265 " pdb=" N GLY E 266 " pdb=" CA GLY E 266 " ideal model delta harmonic sigma weight residual -180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 16116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2086 0.128 - 0.256: 428 0.256 - 0.384: 42 0.384 - 0.512: 15 0.512 - 0.640: 6 Chirality restraints: 2577 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.30e+02 ... (remaining 2574 not shown) Planarity restraints: 5031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " 0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG Q 1 " -0.103 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG O 1 " 0.104 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG M 1 " 0.103 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.218 2.00e-02 2.50e+03 ... (remaining 5028 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 441 1.91 - 2.58: 33066 2.58 - 3.25: 100315 3.25 - 3.93: 135562 3.93 - 4.60: 206358 Nonbonded interactions: 475742 Sorted by model distance: nonbonded pdb=" H CYS C 97 " pdb=" HH TYR C 148 " model vdw 1.235 2.100 nonbonded pdb=" H CYS F 97 " pdb=" HH TYR F 148 " model vdw 1.235 2.100 nonbonded pdb=" H CYS E 97 " pdb=" HH TYR E 148 " model vdw 1.235 2.100 nonbonded pdb=" HH TYR H 59 " pdb=" H ILE H 69 " model vdw 1.304 2.100 nonbonded pdb=" HH TYR G 59 " pdb=" H ILE G 69 " model vdw 1.304 2.100 ... (remaining 475737 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' 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' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.200 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.250 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 : 0.019 0.121 17283 Z= 1.045 Angle : 1.764 24.635 23463 Z= 1.152 Chirality : 0.107 0.640 2577 Planarity : 0.014 0.313 2991 Dihedral : 10.410 87.637 6528 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.80 (0.17), residues: 2100 helix: 0.82 (0.25), residues: 369 sheet: 0.45 (0.20), residues: 537 loop : 0.64 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 38 TYR 0.070 0.011 TYR D 34 PHE 0.028 0.007 PHE E 118 TRP 0.043 0.009 TRP I 103 HIS 0.010 0.002 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.01914 / 1.04 (17241) covalent geometry : angle 1.71919 / 1.15 (23361) SS BOND : bond 0.00929 / 0.60 ( 24) SS BOND : angle 3.34766 / 2.11 ( 48) hydrogen bonds : bond 0.16606 / 11.28 ( 723) hydrogen bonds : angle 7.88482 / 5.63 ( 1980) link_BETA1-4 : bond 0.08103 / 3.75 ( 3) link_BETA1-4 : angle 4.84987 / 2.79 ( 9) link_BETA1-6 : bond 0.01584 / 0.73 ( 3) link_BETA1-6 : angle 7.98489 / 4.22 ( 9) link_NAG-ASN : bond 0.09237 / 6.02 ( 12) link_NAG-ASN : angle 8.61142 / 5.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LEU cc_start: 0.8416 (mt) cc_final: 0.8200 (mt) REVERT: D 158 ASP cc_start: 0.8883 (t0) cc_final: 0.8665 (t0) REVERT: C 71 LEU cc_start: 0.8513 (mt) cc_final: 0.8263 (mt) REVERT: J 14 PHE cc_start: 0.7632 (p90) cc_final: 0.7180 (p90) REVERT: A 158 ASP cc_start: 0.8871 (t0) cc_final: 0.8641 (t0) REVERT: F 17 TYR cc_start: 0.5855 (p90) cc_final: 0.5392 (p90) REVERT: F 71 LEU cc_start: 0.8566 (mt) cc_final: 0.8270 (mt) REVERT: F 131 ASP cc_start: 0.7454 (t0) cc_final: 0.7247 (t0) REVERT: K 82 ASP cc_start: 0.7864 (m-30) cc_final: 0.7462 (m-30) REVERT: B 158 ASP cc_start: 0.8884 (t0) cc_final: 0.8672 (t0) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.3429 time to fit residues: 264.9456 Evaluate side-chains 315 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 ASN E 170 ASN E 298 HIS C 73 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS F 73 ASN F 170 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.142892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.117010 restraints weight = 93049.571| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.23 r_work: 0.3925 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17283 Z= 0.183 Angle : 0.925 34.187 23463 Z= 0.442 Chirality : 0.047 0.238 2577 Planarity : 0.004 0.028 2991 Dihedral : 6.648 59.755 2661 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.14 % Favored : 97.71 % Rotamer: Outliers : 1.31 % Allowed : 7.83 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2100 helix: 2.10 (0.26), residues: 366 sheet: -0.07 (0.19), residues: 579 loop : 0.12 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.017 0.002 TYR F 105 PHE 0.027 0.002 PHE G 100 TRP 0.011 0.002 TRP D 14 HIS 0.010 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (17241) covalent geometry : angle 0.72592 / 0.40 (23361) SS BOND : bond 0.00258 / 0.15 ( 24) SS BOND : angle 1.36697 / 0.77 ( 48) hydrogen bonds : bond 0.06353 / 4.28 ( 723) hydrogen bonds : angle 6.20764 / 4.44 ( 1980) link_BETA1-4 : bond 0.02079 / 0.92 ( 3) link_BETA1-4 : angle 3.52536 / 2.11 ( 9) link_BETA1-6 : bond 0.02181 / 1.02 ( 3) link_BETA1-6 : angle 2.49603 / 1.26 ( 9) link_NAG-ASN : bond 0.00593 / 0.39 ( 12) link_NAG-ASN : angle 14.44508 / 8.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7976 (m100) cc_final: 0.7685 (m100) REVERT: L 83 ILE cc_start: 0.8926 (mt) cc_final: 0.8607 (mm) REVERT: H 35 SER cc_start: 0.8191 (p) cc_final: 0.7903 (t) REVERT: D 158 ASP cc_start: 0.8925 (t0) cc_final: 0.8651 (t0) REVERT: C 25 THR cc_start: 0.7674 (p) cc_final: 0.7313 (t) REVERT: C 208 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8019 (mtp-110) REVERT: C 224 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7670 (ttm110) REVERT: C 256 TYR cc_start: 0.8416 (m-80) cc_final: 0.8204 (m-10) REVERT: J 14 PHE cc_start: 0.6722 (p90) cc_final: 0.5812 (p90) REVERT: J 17 ASP cc_start: 0.7823 (t0) cc_final: 0.7297 (m-30) REVERT: A 74 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 120 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9057 (mm-30) REVERT: A 158 ASP cc_start: 0.8803 (t0) cc_final: 0.8484 (t0) REVERT: F 17 TYR cc_start: 0.5354 (p90) cc_final: 0.4898 (p90) REVERT: F 105 TYR cc_start: 0.7805 (t80) cc_final: 0.7299 (t80) REVERT: K 70 ASP cc_start: 0.7437 (t70) cc_final: 0.7186 (t70) REVERT: B 27 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8413 (pp30) REVERT: B 120 GLU cc_start: 0.9307 (mt-10) cc_final: 0.9038 (mm-30) REVERT: B 138 PHE cc_start: 0.8632 (m-80) cc_final: 0.8382 (m-80) REVERT: B 158 ASP cc_start: 0.8939 (t0) cc_final: 0.8680 (t0) outliers start: 24 outliers final: 16 residues processed: 363 average time/residue: 0.3200 time to fit residues: 172.6705 Evaluate side-chains 314 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain B residue 141 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** 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 = 0.4442 r_free = 0.4442 target = 0.142382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.116558 restraints weight = 92395.717| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.21 r_work: 0.3919 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17283 Z= 0.127 Angle : 0.838 37.118 23463 Z= 0.380 Chirality : 0.043 0.217 2577 Planarity : 0.003 0.026 2991 Dihedral : 5.993 58.672 2661 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 10.07 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.35 (0.17), residues: 2100 helix: 2.32 (0.27), residues: 366 sheet: -0.26 (0.20), residues: 543 loop : -0.12 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 255 TYR 0.025 0.002 TYR D 22 PHE 0.021 0.002 PHE G 100 TRP 0.006 0.001 TRP G 47 HIS 0.006 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (17241) covalent geometry : angle 0.58680 / 0.32 (23361) SS BOND : bond 0.00387 / 0.23 ( 24) SS BOND : angle 1.63532 / 1.04 ( 48) hydrogen bonds : bond 0.05093 / 3.40 ( 723) hydrogen bonds : angle 5.79932 / 4.16 ( 1980) link_BETA1-4 : bond 0.00115 / 0.05 ( 3) link_BETA1-4 : angle 1.25623 / 0.73 ( 9) link_BETA1-6 : bond 0.00810 / 0.40 ( 3) link_BETA1-6 : angle 2.41775 / 1.20 ( 9) link_NAG-ASN : bond 0.00528 / 0.35 ( 12) link_NAG-ASN : angle 15.11988 / 9.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7840 (tt) REVERT: L 83 ILE cc_start: 0.8881 (mt) cc_final: 0.8553 (mm) REVERT: H 34 MET cc_start: 0.8270 (mmt) cc_final: 0.7948 (mmt) REVERT: H 35 SER cc_start: 0.8307 (p) cc_final: 0.8011 (t) REVERT: H 79 TYR cc_start: 0.8357 (m-80) cc_final: 0.7953 (m-10) REVERT: D 132 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7421 (mp0) REVERT: C 208 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7989 (mtp-110) REVERT: C 224 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7536 (ttm110) REVERT: J 14 PHE cc_start: 0.6683 (p90) cc_final: 0.5856 (p90) REVERT: J 17 ASP cc_start: 0.7870 (t0) cc_final: 0.7461 (m-30) REVERT: J 36 TYR cc_start: 0.7902 (m-80) cc_final: 0.7218 (m-80) REVERT: G 35 SER cc_start: 0.8129 (p) cc_final: 0.7863 (t) REVERT: A 74 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 158 ASP cc_start: 0.8749 (t0) cc_final: 0.8427 (t0) REVERT: F 17 TYR cc_start: 0.5438 (p90) cc_final: 0.4992 (p90) REVERT: F 105 TYR cc_start: 0.7975 (t80) cc_final: 0.7673 (t80) REVERT: I 35 SER cc_start: 0.8248 (p) cc_final: 0.7986 (t) REVERT: I 101 GLU cc_start: 0.6950 (tt0) cc_final: 0.6604 (tp30) REVERT: B 27 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8455 (pp30) REVERT: B 120 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9030 (mm-30) REVERT: B 158 ASP cc_start: 0.8762 (t0) cc_final: 0.8440 (t0) outliers start: 23 outliers final: 16 residues processed: 328 average time/residue: 0.3216 time to fit residues: 154.7725 Evaluate side-chains 303 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 141 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.113305 restraints weight = 92901.777| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.08 r_work: 0.3866 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17283 Z= 0.203 Angle : 0.856 38.646 23463 Z= 0.388 Chirality : 0.043 0.263 2577 Planarity : 0.004 0.044 2991 Dihedral : 6.061 56.519 2661 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 9.91 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.05 (0.17), residues: 2100 helix: 1.98 (0.26), residues: 366 sheet: -0.36 (0.20), residues: 576 loop : -0.33 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 100E TYR 0.024 0.002 TYR C 256 PHE 0.017 0.002 PHE L 14 TRP 0.011 0.002 TRP B 21 HIS 0.006 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (17241) covalent geometry : angle 0.59194 / 0.33 (23361) SS BOND : bond 0.00589 / 0.37 ( 24) SS BOND : angle 1.72905 / 1.02 ( 48) hydrogen bonds : bond 0.04742 / 3.19 ( 723) hydrogen bonds : angle 5.58532 / 4.01 ( 1980) link_BETA1-4 : bond 0.00067 / 0.03 ( 3) link_BETA1-4 : angle 1.16101 / 0.62 ( 9) link_BETA1-6 : bond 0.00442 / 0.21 ( 3) link_BETA1-6 : angle 1.66498 / 0.81 ( 9) link_NAG-ASN : bond 0.00221 / 0.14 ( 12) link_NAG-ASN : angle 15.67453 / 9.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8229 (pt0) cc_final: 0.7978 (pt0) REVERT: E 105 TYR cc_start: 0.8134 (t80) cc_final: 0.7928 (t80) REVERT: L 81 GLU cc_start: 0.8896 (mp0) cc_final: 0.8631 (mp0) REVERT: L 83 ILE cc_start: 0.8963 (mt) cc_final: 0.8649 (mm) REVERT: H 35 SER cc_start: 0.8372 (p) cc_final: 0.8058 (t) REVERT: H 79 TYR cc_start: 0.8324 (m-80) cc_final: 0.7827 (m-10) REVERT: D 74 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 105 TYR cc_start: 0.8237 (t80) cc_final: 0.7946 (t80) REVERT: C 208 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8084 (mtp-110) REVERT: C 224 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7768 (ttm110) REVERT: J 14 PHE cc_start: 0.6785 (p90) cc_final: 0.5942 (p90) REVERT: J 17 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: J 36 TYR cc_start: 0.7977 (m-80) cc_final: 0.7291 (m-80) REVERT: G 35 SER cc_start: 0.8358 (p) cc_final: 0.7945 (t) REVERT: A 132 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7720 (mp0) REVERT: F 17 TYR cc_start: 0.5628 (p90) cc_final: 0.5118 (p90) REVERT: F 105 TYR cc_start: 0.8079 (t80) cc_final: 0.7767 (t80) REVERT: I 35 SER cc_start: 0.8445 (p) cc_final: 0.8084 (t) REVERT: I 79 TYR cc_start: 0.8249 (m-80) cc_final: 0.7901 (m-10) REVERT: B 120 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9048 (mm-30) outliers start: 30 outliers final: 24 residues processed: 307 average time/residue: 0.3312 time to fit residues: 149.0194 Evaluate side-chains 293 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** F 231 ASN ** 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 = 0.4390 r_free = 0.4390 target = 0.138442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.113113 restraints weight = 93266.785| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.15 r_work: 0.3863 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17283 Z= 0.166 Angle : 0.830 38.596 23463 Z= 0.367 Chirality : 0.043 0.258 2577 Planarity : 0.004 0.032 2991 Dihedral : 5.905 54.502 2661 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Rotamer: Outliers : 1.70 % Allowed : 10.56 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.02 (0.17), residues: 2100 helix: 2.03 (0.26), residues: 366 sheet: -0.39 (0.20), residues: 570 loop : -0.43 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100E TYR 0.012 0.002 TYR H 79 PHE 0.017 0.002 PHE L 14 TRP 0.010 0.001 TRP A 21 HIS 0.006 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17241) covalent geometry : angle 0.55567 / 0.30 (23361) SS BOND : bond 0.00395 / 0.25 ( 24) SS BOND : angle 1.11651 / 0.68 ( 48) hydrogen bonds : bond 0.04435 / 2.96 ( 723) hydrogen bonds : angle 5.40184 / 3.88 ( 1980) link_BETA1-4 : bond 0.00194 / 0.09 ( 3) link_BETA1-4 : angle 1.01627 / 0.57 ( 9) link_BETA1-6 : bond 0.00308 / 0.14 ( 3) link_BETA1-6 : angle 1.60603 / 0.78 ( 9) link_NAG-ASN : bond 0.00291 / 0.19 ( 12) link_NAG-ASN : angle 15.67526 / 9.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8039 (tt) REVERT: L 81 GLU cc_start: 0.8903 (mp0) cc_final: 0.8649 (mp0) REVERT: L 83 ILE cc_start: 0.8899 (mt) cc_final: 0.8600 (mm) REVERT: H 35 SER cc_start: 0.8336 (p) cc_final: 0.8027 (t) REVERT: H 79 TYR cc_start: 0.8436 (m-80) cc_final: 0.7988 (m-10) REVERT: C 105 TYR cc_start: 0.8235 (t80) cc_final: 0.7994 (t80) REVERT: C 208 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.8050 (mtp-110) REVERT: C 224 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7631 (ttm110) REVERT: J 14 PHE cc_start: 0.6895 (p90) cc_final: 0.6088 (p90) REVERT: J 17 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: J 36 TYR cc_start: 0.7950 (m-80) cc_final: 0.7224 (m-80) REVERT: G 35 SER cc_start: 0.8292 (p) cc_final: 0.7976 (t) REVERT: F 105 TYR cc_start: 0.8033 (t80) cc_final: 0.7732 (t80) REVERT: I 35 SER cc_start: 0.8383 (p) cc_final: 0.8061 (t) REVERT: I 79 TYR cc_start: 0.8320 (m-80) cc_final: 0.8065 (m-10) REVERT: B 120 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9094 (mm-30) outliers start: 31 outliers final: 22 residues processed: 297 average time/residue: 0.3226 time to fit residues: 140.3829 Evaluate side-chains 290 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 107 optimal weight: 0.0980 chunk 117 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 181 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.3533 > 50:) overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.140297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115023 restraints weight = 92285.598| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.14 r_work: 0.3894 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17283 Z= 0.104 Angle : 0.800 38.709 23463 Z= 0.346 Chirality : 0.042 0.226 2577 Planarity : 0.003 0.027 2991 Dihedral : 5.659 54.153 2661 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.10 % Favored : 96.76 % Rotamer: Outliers : 1.59 % Allowed : 11.11 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.00 (0.17), residues: 2100 helix: 2.27 (0.26), residues: 363 sheet: -0.39 (0.21), residues: 519 loop : -0.49 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 208 TYR 0.024 0.001 TYR E 105 PHE 0.032 0.001 PHE F 147 TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17241) covalent geometry : angle 0.51250 / 0.28 (23361) SS BOND : bond 0.00224 / 0.13 ( 24) SS BOND : angle 0.83581 / 0.51 ( 48) hydrogen bonds : bond 0.04080 / 2.70 ( 723) hydrogen bonds : angle 5.18310 / 3.72 ( 1980) link_BETA1-4 : bond 0.00289 / 0.13 ( 3) link_BETA1-4 : angle 0.99947 / 0.57 ( 9) link_BETA1-6 : bond 0.00325 / 0.15 ( 3) link_BETA1-6 : angle 1.26121 / 0.63 ( 9) link_NAG-ASN : bond 0.00294 / 0.20 ( 12) link_NAG-ASN : angle 15.66853 / 9.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8305 (pt0) cc_final: 0.8029 (pt0) REVERT: E 79 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8037 (tt) REVERT: E 225 ASP cc_start: 0.6843 (t0) cc_final: 0.6616 (t0) REVERT: L 81 GLU cc_start: 0.8913 (mp0) cc_final: 0.8659 (mp0) REVERT: H 35 SER cc_start: 0.8347 (p) cc_final: 0.8024 (t) REVERT: H 50 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8137 (ptm) REVERT: H 79 TYR cc_start: 0.8420 (m-80) cc_final: 0.7930 (m-80) REVERT: D 118 LEU cc_start: 0.8481 (mm) cc_final: 0.8279 (mp) REVERT: C 167 SER cc_start: 0.9039 (p) cc_final: 0.8658 (m) REVERT: C 208 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8052 (mtp-110) REVERT: C 224 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7831 (ttm110) REVERT: J 14 PHE cc_start: 0.6873 (p90) cc_final: 0.6106 (p90) REVERT: J 17 ASP cc_start: 0.7968 (t0) cc_final: 0.7634 (m-30) REVERT: G 35 SER cc_start: 0.8238 (p) cc_final: 0.7947 (t) REVERT: G 64 LYS cc_start: 0.8905 (tttt) cc_final: 0.8621 (tptp) REVERT: G 101 GLU cc_start: 0.6957 (tt0) cc_final: 0.6303 (tp30) REVERT: F 105 TYR cc_start: 0.7966 (t80) cc_final: 0.7654 (t80) REVERT: I 35 SER cc_start: 0.8355 (p) cc_final: 0.8053 (t) REVERT: I 101 GLU cc_start: 0.7033 (tt0) cc_final: 0.6512 (tp30) REVERT: B 120 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9119 (mm-30) outliers start: 29 outliers final: 19 residues processed: 300 average time/residue: 0.3245 time to fit residues: 143.2739 Evaluate side-chains 293 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** F 231 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.136664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.111256 restraints weight = 93294.961| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.16 r_work: 0.3830 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17283 Z= 0.193 Angle : 0.841 38.929 23463 Z= 0.372 Chirality : 0.042 0.250 2577 Planarity : 0.004 0.045 2991 Dihedral : 5.778 55.757 2661 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 11.99 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.28 (0.17), residues: 2100 helix: 2.08 (0.26), residues: 363 sheet: -0.59 (0.21), residues: 525 loop : -0.68 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100E TYR 0.018 0.002 TYR C 233 PHE 0.018 0.002 PHE L 14 TRP 0.009 0.002 TRP A 21 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17241) covalent geometry : angle 0.56607 / 0.31 (23361) SS BOND : bond 0.00460 / 0.29 ( 24) SS BOND : angle 1.07974 / 0.63 ( 48) hydrogen bonds : bond 0.04284 / 2.86 ( 723) hydrogen bonds : angle 5.23481 / 3.75 ( 1980) link_BETA1-4 : bond 0.00163 / 0.08 ( 3) link_BETA1-4 : angle 0.99023 / 0.52 ( 9) link_BETA1-6 : bond 0.00326 / 0.16 ( 3) link_BETA1-6 : angle 1.56360 / 0.76 ( 9) link_NAG-ASN : bond 0.00222 / 0.14 ( 12) link_NAG-ASN : angle 15.84840 / 9.83 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8302 (pt0) cc_final: 0.8092 (pt0) REVERT: E 79 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8092 (tt) REVERT: L 81 GLU cc_start: 0.8906 (mp0) cc_final: 0.8660 (mp0) REVERT: H 35 SER cc_start: 0.8348 (p) cc_final: 0.8063 (t) REVERT: H 50 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8216 (ptm) REVERT: H 79 TYR cc_start: 0.8411 (m-80) cc_final: 0.7941 (m-80) REVERT: C 105 TYR cc_start: 0.8310 (t80) cc_final: 0.8052 (t80) REVERT: C 167 SER cc_start: 0.9100 (p) cc_final: 0.8733 (m) REVERT: C 208 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8087 (mtp-110) REVERT: C 224 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7867 (ttm110) REVERT: J 14 PHE cc_start: 0.6923 (p90) cc_final: 0.6152 (p90) REVERT: J 17 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: J 81 GLU cc_start: 0.8722 (mp0) cc_final: 0.8421 (mp0) REVERT: G 35 SER cc_start: 0.8324 (p) cc_final: 0.8002 (t) REVERT: G 64 LYS cc_start: 0.8929 (tttt) cc_final: 0.8593 (tptt) REVERT: F 105 TYR cc_start: 0.8085 (t80) cc_final: 0.7794 (t80) REVERT: I 35 SER cc_start: 0.8340 (p) cc_final: 0.7999 (t) REVERT: B 120 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9124 (mm-30) outliers start: 27 outliers final: 23 residues processed: 285 average time/residue: 0.3221 time to fit residues: 134.9555 Evaluate side-chains 285 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.135053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.109956 restraints weight = 93723.848| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.07 r_work: 0.3807 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17283 Z= 0.221 Angle : 0.850 38.809 23463 Z= 0.379 Chirality : 0.043 0.267 2577 Planarity : 0.004 0.047 2991 Dihedral : 5.881 54.891 2661 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 1.64 % Allowed : 12.15 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.57 (0.17), residues: 2100 helix: 1.89 (0.25), residues: 363 sheet: -0.76 (0.21), residues: 510 loop : -0.90 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100E TYR 0.015 0.002 TYR C 148 PHE 0.036 0.002 PHE C 147 TRP 0.012 0.002 TRP A 21 HIS 0.004 0.001 HIS F 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (17241) covalent geometry : angle 0.57707 / 0.32 (23361) SS BOND : bond 0.00514 / 0.34 ( 24) SS BOND : angle 1.20711 / 0.72 ( 48) hydrogen bonds : bond 0.04312 / 2.90 ( 723) hydrogen bonds : angle 5.29312 / 3.79 ( 1980) link_BETA1-4 : bond 0.00158 / 0.07 ( 3) link_BETA1-4 : angle 1.00820 / 0.55 ( 9) link_BETA1-6 : bond 0.00225 / 0.10 ( 3) link_BETA1-6 : angle 1.50618 / 0.73 ( 9) link_NAG-ASN : bond 0.00259 / 0.16 ( 12) link_NAG-ASN : angle 15.87870 / 9.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8271 (pt0) cc_final: 0.8053 (pt0) REVERT: E 79 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8108 (tt) REVERT: L 81 GLU cc_start: 0.9007 (mp0) cc_final: 0.8759 (mp0) REVERT: H 35 SER cc_start: 0.8347 (p) cc_final: 0.8066 (t) REVERT: H 50 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8266 (ptm) REVERT: H 79 TYR cc_start: 0.8442 (m-80) cc_final: 0.7985 (m-80) REVERT: C 105 TYR cc_start: 0.8368 (t80) cc_final: 0.8099 (t80) REVERT: C 224 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7828 (ttm110) REVERT: J 17 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: J 81 GLU cc_start: 0.8833 (mp0) cc_final: 0.8565 (mp0) REVERT: G 35 SER cc_start: 0.8280 (p) cc_final: 0.7913 (t) REVERT: G 64 LYS cc_start: 0.8963 (tttt) cc_final: 0.8636 (tptt) REVERT: A 17 MET cc_start: 0.3522 (ttm) cc_final: 0.2916 (ttm) REVERT: F 105 TYR cc_start: 0.8185 (t80) cc_final: 0.7852 (t80) REVERT: I 35 SER cc_start: 0.8362 (p) cc_final: 0.7973 (t) REVERT: B 120 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9116 (mm-30) outliers start: 30 outliers final: 25 residues processed: 284 average time/residue: 0.3340 time to fit residues: 139.7592 Evaluate side-chains 290 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 144 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.109922 restraints weight = 93807.150| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.06 r_work: 0.3801 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17283 Z= 0.209 Angle : 0.850 38.804 23463 Z= 0.378 Chirality : 0.043 0.266 2577 Planarity : 0.004 0.042 2991 Dihedral : 5.848 55.108 2661 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 1.81 % Allowed : 12.10 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.76 (0.17), residues: 2100 helix: 1.76 (0.25), residues: 369 sheet: -0.90 (0.21), residues: 522 loop : -1.04 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 100E TYR 0.013 0.002 TYR H 79 PHE 0.029 0.002 PHE L 14 TRP 0.011 0.002 TRP C 153 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (17241) covalent geometry : angle 0.57630 / 0.32 (23361) SS BOND : bond 0.00571 / 0.40 ( 24) SS BOND : angle 1.22788 / 0.69 ( 48) hydrogen bonds : bond 0.04223 / 2.84 ( 723) hydrogen bonds : angle 5.26883 / 3.77 ( 1980) link_BETA1-4 : bond 0.00154 / 0.07 ( 3) link_BETA1-4 : angle 0.95783 / 0.52 ( 9) link_BETA1-6 : bond 0.00247 / 0.11 ( 3) link_BETA1-6 : angle 1.47853 / 0.72 ( 9) link_NAG-ASN : bond 0.00312 / 0.19 ( 12) link_NAG-ASN : angle 15.88810 / 9.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8131 (tt) REVERT: L 14 PHE cc_start: 0.6649 (p90) cc_final: 0.6384 (p90) REVERT: L 17 ASP cc_start: 0.7448 (m-30) cc_final: 0.6972 (m-30) REVERT: L 81 GLU cc_start: 0.9028 (mp0) cc_final: 0.8783 (mp0) REVERT: H 35 SER cc_start: 0.8351 (p) cc_final: 0.8064 (t) REVERT: H 50 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8212 (ptm) REVERT: H 79 TYR cc_start: 0.8439 (m-80) cc_final: 0.7986 (m-80) REVERT: D 123 ARG cc_start: 0.8520 (tpt-90) cc_final: 0.7974 (ttm110) REVERT: C 105 TYR cc_start: 0.8350 (t80) cc_final: 0.8073 (t80) REVERT: C 224 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7860 (ttm110) REVERT: J 17 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: J 81 GLU cc_start: 0.8853 (mp0) cc_final: 0.8586 (mp0) REVERT: G 35 SER cc_start: 0.8198 (p) cc_final: 0.7820 (t) REVERT: G 64 LYS cc_start: 0.8935 (tttt) cc_final: 0.8598 (tptt) REVERT: G 79 TYR cc_start: 0.8369 (m-10) cc_final: 0.7861 (m-10) REVERT: A 17 MET cc_start: 0.3507 (ttm) cc_final: 0.2948 (ttm) REVERT: A 118 LEU cc_start: 0.8431 (mm) cc_final: 0.8189 (mp) REVERT: F 105 TYR cc_start: 0.8241 (t80) cc_final: 0.7896 (t80) REVERT: K 17 ASP cc_start: 0.8044 (m-30) cc_final: 0.7752 (m-30) REVERT: I 35 SER cc_start: 0.8359 (p) cc_final: 0.7970 (t) REVERT: B 120 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9108 (mm-30) outliers start: 33 outliers final: 28 residues processed: 280 average time/residue: 0.3318 time to fit residues: 137.4562 Evaluate side-chains 282 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.136766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.111771 restraints weight = 93411.469| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.09 r_work: 0.3833 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17283 Z= 0.126 Angle : 0.823 38.810 23463 Z= 0.360 Chirality : 0.042 0.242 2577 Planarity : 0.004 0.038 2991 Dihedral : 5.629 53.858 2661 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.67 % Rotamer: Outliers : 1.42 % Allowed : 12.92 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.63 (0.17), residues: 2100 helix: 1.87 (0.26), residues: 369 sheet: -0.83 (0.21), residues: 522 loop : -0.95 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 208 TYR 0.012 0.001 TYR F 105 PHE 0.028 0.002 PHE C 147 TRP 0.008 0.001 TRP D 21 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (17241) covalent geometry : angle 0.53697 / 0.29 (23361) SS BOND : bond 0.00542 / 0.34 ( 24) SS BOND : angle 1.63839 / 0.99 ( 48) hydrogen bonds : bond 0.03958 / 2.65 ( 723) hydrogen bonds : angle 5.16663 / 3.69 ( 1980) link_BETA1-4 : bond 0.00298 / 0.14 ( 3) link_BETA1-4 : angle 0.97676 / 0.53 ( 9) link_BETA1-6 : bond 0.00372 / 0.17 ( 3) link_BETA1-6 : angle 1.27431 / 0.64 ( 9) link_NAG-ASN : bond 0.00317 / 0.21 ( 12) link_NAG-ASN : angle 15.81534 / 9.82 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7366 (m-30) cc_final: 0.6913 (m-30) REVERT: L 81 GLU cc_start: 0.9065 (mp0) cc_final: 0.8852 (mp0) REVERT: H 35 SER cc_start: 0.8281 (p) cc_final: 0.8032 (t) REVERT: H 50 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8202 (ptm) REVERT: H 79 TYR cc_start: 0.8443 (m-80) cc_final: 0.8011 (m-80) REVERT: D 123 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.7969 (ttm110) REVERT: C 224 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7864 (ttm110) REVERT: J 17 ASP cc_start: 0.8111 (t0) cc_final: 0.7783 (m-30) REVERT: J 45 LYS cc_start: 0.7177 (tttt) cc_final: 0.6919 (tttp) REVERT: J 81 GLU cc_start: 0.8858 (mp0) cc_final: 0.8602 (mp0) REVERT: G 35 SER cc_start: 0.8226 (p) cc_final: 0.7908 (t) REVERT: G 64 LYS cc_start: 0.8939 (tttt) cc_final: 0.8637 (tptp) REVERT: A 118 LEU cc_start: 0.8431 (mm) cc_final: 0.8195 (mp) REVERT: K 17 ASP cc_start: 0.8023 (m-30) cc_final: 0.7659 (m-30) REVERT: I 35 SER cc_start: 0.8358 (p) cc_final: 0.8045 (t) REVERT: B 120 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9089 (mm-30) outliers start: 26 outliers final: 23 residues processed: 277 average time/residue: 0.3484 time to fit residues: 141.6979 Evaluate side-chains 277 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 179 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 73 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** 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 = 0.4351 r_free = 0.4351 target = 0.135842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.110818 restraints weight = 93701.636| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.09 r_work: 0.3817 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17283 Z= 0.166 Angle : 0.831 38.883 23463 Z= 0.365 Chirality : 0.042 0.245 2577 Planarity : 0.004 0.035 2991 Dihedral : 5.684 54.998 2661 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 1.37 % Allowed : 13.30 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.74 (0.17), residues: 2100 helix: 1.85 (0.26), residues: 369 sheet: -0.85 (0.21), residues: 537 loop : -1.07 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 208 TYR 0.013 0.002 TYR C 148 PHE 0.039 0.002 PHE C 147 TRP 0.009 0.001 TRP C 153 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (17241) covalent geometry : angle 0.54862 / 0.30 (23361) SS BOND : bond 0.00433 / 0.26 ( 24) SS BOND : angle 1.45993 / 0.85 ( 48) hydrogen bonds : bond 0.03969 / 2.66 ( 723) hydrogen bonds : angle 5.32269 / 3.82 ( 1980) link_BETA1-4 : bond 0.00205 / 0.09 ( 3) link_BETA1-4 : angle 0.95961 / 0.51 ( 9) link_BETA1-6 : bond 0.00224 / 0.10 ( 3) link_BETA1-6 : angle 1.35774 / 0.66 ( 9) link_NAG-ASN : bond 0.00241 / 0.15 ( 12) link_NAG-ASN : angle 15.85732 / 9.85 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.40 seconds wall clock time: 136 minutes 17.64 seconds (8177.64 seconds total)