Starting phenix.real_space_refine on Tue Aug 26 03:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_23792_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_23792_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_23792_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_23792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mem_23792/08_2025/7mem_23792.map" } 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-2.0-5787/lib/python3.9/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: 4.96, per 1000 atoms: 0.15 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: 2.88 Conformation dependent library (CDL) restraints added in 839.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.00 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: 8.43 Time building geometry restraints manager: 3.73 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 aren 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 covalent geometry : bond 0.01914 (17241) covalent geometry : angle 1.71919 (23361) SS BOND : bond 0.00929 ( 24) SS BOND : angle 3.34766 ( 48) hydrogen bonds : bond 0.16606 ( 723) hydrogen bonds : angle 7.88482 ( 1980) link_BETA1-4 : bond 0.08103 ( 3) link_BETA1-4 : angle 4.84987 ( 9) link_BETA1-6 : bond 0.01584 ( 3) link_BETA1-6 : angle 7.98489 ( 9) link_NAG-ASN : bond 0.09237 ( 12) link_NAG-ASN : angle 8.61142 ( 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 : 0.786 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: 0.3078 time to fit residues: 234.8194 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 : 0.857 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7038 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 aren 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 covalent geometry : bond 0.00387 (17241) covalent geometry : angle 0.72592 (23361) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.36697 ( 48) hydrogen bonds : bond 0.06353 ( 723) hydrogen bonds : angle 6.20764 ( 1980) link_BETA1-4 : bond 0.02079 ( 3) link_BETA1-4 : angle 3.52536 ( 9) link_BETA1-6 : bond 0.02181 ( 3) link_BETA1-6 : angle 2.49603 ( 9) link_NAG-ASN : bond 0.00593 ( 12) link_NAG-ASN : angle 14.44508 ( 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 : 0.811 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: 0.3273 time to fit residues: 172.1736 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 : 0.878 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7059 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 aren 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 covalent geometry : bond 0.00261 (17241) covalent geometry : angle 0.58680 (23361) SS BOND : bond 0.00387 ( 24) SS BOND : angle 1.63532 ( 48) hydrogen bonds : bond 0.05093 ( 723) hydrogen bonds : angle 5.79932 ( 1980) link_BETA1-4 : bond 0.00115 ( 3) link_BETA1-4 : angle 1.25623 ( 9) link_BETA1-6 : bond 0.00810 ( 3) link_BETA1-6 : angle 2.41775 ( 9) link_NAG-ASN : bond 0.00528 ( 12) link_NAG-ASN : angle 15.11988 ( 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 : 0.794 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: 0.8358 (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: 0.3351 time to fit residues: 158.9506 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 : 0.680 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7094 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 aren 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 covalent geometry : bond 0.00449 (17241) covalent geometry : angle 0.59194 (23361) SS BOND : bond 0.00589 ( 24) SS BOND : angle 1.72905 ( 48) hydrogen bonds : bond 0.04742 ( 723) hydrogen bonds : angle 5.58532 ( 1980) link_BETA1-4 : bond 0.00067 ( 3) link_BETA1-4 : angle 1.16101 ( 9) link_BETA1-6 : bond 0.00442 ( 3) link_BETA1-6 : angle 1.66498 ( 9) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 15.67453 ( 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 : 0.966 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: 0.2958 time to fit residues: 132.0777 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 : 0.918 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7117 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 aren 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 covalent geometry : bond 0.00369 (17241) covalent geometry : angle 0.55567 (23361) SS BOND : bond 0.00395 ( 24) SS BOND : angle 1.11651 ( 48) hydrogen bonds : bond 0.04435 ( 723) hydrogen bonds : angle 5.40184 ( 1980) link_BETA1-4 : bond 0.00194 ( 3) link_BETA1-4 : angle 1.01627 ( 9) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 1.60603 ( 9) link_NAG-ASN : bond 0.00291 ( 12) link_NAG-ASN : angle 15.67526 ( 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 : 0.619 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: 0.7532 (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: 0.2875 time to fit residues: 123.3635 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 : 0.805 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3533 > 50: distance: 205 - 220: 11.521 distance: 220 - 221: 8.331 distance: 220 - 230: 6.956 distance: 220 - 349: 16.669 distance: 221 - 222: 6.765 distance: 221 - 224: 4.871 distance: 221 - 231: 8.851 distance: 222 - 223: 11.445 distance: 222 - 237: 6.113 distance: 224 - 225: 4.876 distance: 224 - 232: 18.534 distance: 225 - 226: 7.258 distance: 226 - 228: 5.065 distance: 227 - 229: 8.501 distance: 227 - 234: 3.544 distance: 228 - 229: 6.128 distance: 228 - 235: 5.224 distance: 229 - 236: 3.029 distance: 237 - 238: 5.664 distance: 237 - 249: 13.956 distance: 238 - 239: 9.857 distance: 238 - 241: 6.976 distance: 238 - 250: 19.210 distance: 239 - 240: 22.755 distance: 239 - 258: 6.823 distance: 241 - 242: 9.149 distance: 241 - 251: 7.567 distance: 241 - 252: 3.175 distance: 242 - 243: 8.563 distance: 242 - 244: 7.491 distance: 243 - 245: 5.339 distance: 243 - 253: 6.289 distance: 244 - 246: 3.479 distance: 244 - 254: 4.870 distance: 245 - 247: 4.060 distance: 246 - 247: 3.355 distance: 246 - 256: 4.753 distance: 247 - 248: 5.939 distance: 248 - 257: 6.984 distance: 258 - 259: 3.258 distance: 258 - 268: 15.950 distance: 259 - 260: 8.515 distance: 259 - 262: 3.806 distance: 259 - 269: 12.851 distance: 260 - 261: 21.449 distance: 260 - 275: 8.710 distance: 262 - 263: 7.662 distance: 262 - 270: 23.791 distance: 262 - 271: 18.291 distance: 263 - 265: 15.801 distance: 264 - 266: 9.219 distance: 264 - 272: 6.521 distance: 265 - 267: 4.061 distance: 265 - 273: 10.838 distance: 266 - 267: 8.351 distance: 266 - 274: 7.009 distance: 275 - 276: 15.470 distance: 275 - 283: 19.873 distance: 276 - 277: 10.648 distance: 276 - 279: 11.238 distance: 276 - 284: 5.885 distance: 277 - 278: 4.923 distance: 277 - 289: 26.575 distance: 279 - 280: 8.812 distance: 279 - 285: 14.133 distance: 279 - 286: 17.401 distance: 280 - 281: 6.601 distance: 280 - 282: 6.355 distance: 282 - 287: 16.622 distance: 282 - 288: 3.441 distance: 289 - 290: 21.603 distance: 289 - 297: 22.849 distance: 290 - 291: 10.749 distance: 290 - 293: 16.917 distance: 290 - 298: 4.753 distance: 291 - 292: 19.755 distance: 291 - 308: 32.870 distance: 293 - 294: 18.971 distance: 293 - 299: 18.187 distance: 293 - 300: 11.279 distance: 294 - 295: 6.156 distance: 294 - 296: 13.791 distance: 294 - 301: 14.876 distance: 295 - 302: 4.182 distance: 295 - 303: 13.043 distance: 295 - 304: 11.778 distance: 296 - 305: 15.144 distance: 296 - 306: 11.097 distance: 296 - 307: 8.793 distance: 308 - 309: 25.820 distance: 308 - 314: 23.064 distance: 309 - 310: 21.028 distance: 309 - 312: 21.664 distance: 309 - 315: 12.580 distance: 310 - 311: 20.328 distance: 310 - 322: 31.077 distance: 312 - 313: 13.173 distance: 312 - 316: 31.776 distance: 312 - 317: 6.173 distance: 313 - 314: 20.586 distance: 313 - 318: 18.688 distance: 313 - 319: 14.561 distance: 314 - 320: 21.398 distance: 314 - 321: 14.855 distance: 322 - 323: 25.735 distance: 322 - 333: 30.602 distance: 323 - 324: 14.898 distance: 323 - 326: 24.142 distance: 323 - 334: 19.245 distance: 324 - 325: 8.303 distance: 324 - 346: 10.070 distance: 326 - 327: 14.694 distance: 326 - 335: 37.255 distance: 326 - 336: 17.293 distance: 327 - 328: 7.690 distance: 327 - 337: 4.385 distance: 327 - 338: 9.718 distance: 328 - 329: 5.146 distance: 328 - 339: 7.618 distance: 328 - 340: 9.541 distance: 329 - 330: 3.048 distance: 329 - 341: 9.615 distance: 330 - 331: 5.199 distance: 330 - 332: 5.764 distance: 331 - 342: 3.596 distance: 331 - 343: 3.500 distance: 332 - 344: 4.038 distance: 332 - 345: 3.711 distance: 346 - 347: 16.661 distance: 346 - 353: 13.039 distance: 347 - 348: 19.791 distance: 347 - 350: 9.050 distance: 347 - 354: 18.563 distance: 348 - 349: 11.397 distance: 348 - 360: 5.621 distance: 350 - 351: 25.947 distance: 350 - 352: 24.266 distance: 350 - 355: 20.465 distance: 351 - 356: 7.876 distance: 352 - 357: 7.904 distance: 352 - 358: 4.130 distance: 352 - 359: 15.582 distance: 360 - 361: 3.711 distance: 360 - 371: 6.043 distance: 361 - 362: 12.069 distance: 361 - 364: 19.261 distance: 361 - 372: 8.410 distance: 362 - 363: 14.697 distance: 362 - 380: 21.625 distance: 364 - 365: 5.457 distance: 364 - 373: 16.567 distance: 364 - 374: 17.886 distance: 365 - 366: 13.007 distance: 365 - 367: 10.495 distance: 366 - 368: 11.113 distance: 366 - 375: 7.555 distance: 367 - 369: 10.582 distance: 367 - 376: 6.002 distance: 368 - 370: 8.272 distance: 368 - 377: 8.047 distance: 369 - 370: 16.345 distance: 369 - 378: 9.832 distance: 370 - 379: 4.746 distance: 380 - 381: 28.403 distance: 380 - 384: 20.646 distance: 381 - 382: 9.456 distance: 381 - 385: 37.267 distance: 381 - 386: 51.369 distance: 382 - 383: 15.282 distance: 382 - 387: 20.651