Starting phenix.real_space_refine on Wed Jan 22 21:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3b_22655/01_2025/7k3b_22655.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 11901 2.51 5 N 3192 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19038 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" 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: "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 Time building chain proxies: 13.04, per 1000 atoms: 0.68 Number of scatterers: 19038 At special positions: 0 Unit cell: (184.87, 186.2, 127.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3864 8.00 N 3192 7.00 C 11901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.5 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 63 sheets defined 16.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 75 through 125 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.244A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.669A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.557A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.689A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.763A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.514A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.697A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.710A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.668A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.578A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.044A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.669A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.517A pdb=" N LYS D 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.670A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.646A pdb=" N LYS F 62 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.294A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.601A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL G 138 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU G 184 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU G 140 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 182 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN G 142 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 180 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.291A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.454A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.703A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 191 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 161 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.562A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 17 through 22 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.531A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 160 removed outlier: 4.438A pdb=" N TRP K 153 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 210 " --> pdb=" O VAL K 201 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL L 191 " --> pdb=" O HIS L 174 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 161 through 164 779 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6038 1.34 - 1.46: 4512 1.46 - 1.58: 8770 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 19434 Sorted by residual: bond pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA O 3 " pdb=" C4 BMA O 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA U 3 " pdb=" C4 BMA U 3 " ideal model delta sigma weight residual 1.541 1.504 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.442 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.441 -0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 19429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 24943 1.46 - 2.92: 1152 2.92 - 4.37: 228 4.37 - 5.83: 55 5.83 - 7.29: 40 Bond angle restraints: 26418 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" N LYS G 195 " pdb=" CA LYS G 195 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLY B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" C GLY F 50 " pdb=" N LYS F 51 " pdb=" CA LYS F 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C GLY D 50 " pdb=" N LYS D 51 " pdb=" CA LYS D 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.79e+00 angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 126.47 -4.93 1.91e+00 2.74e-01 6.65e+00 ... (remaining 26413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 11595 23.02 - 46.04: 572 46.04 - 69.06: 63 69.06 - 92.08: 52 92.08 - 115.10: 24 Dihedral angle restraints: 12306 sinusoidal: 5436 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 37.38 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 40.51 52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA GLN I 81 " pdb=" C GLN I 81 " pdb=" N ALA I 82 " pdb=" CA ALA I 82 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 12303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2631 0.069 - 0.137: 489 0.137 - 0.206: 15 0.206 - 0.274: 15 0.274 - 0.343: 3 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C1 NAG E 401 " pdb=" ND2 ASN E 22 " pdb=" C2 NAG E 401 " pdb=" O5 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 22 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3150 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 194 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO J 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 195 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 194 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO H 195 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 195 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 195 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 194 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO L 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 195 " 0.021 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 867 2.70 - 3.25: 18430 3.25 - 3.80: 31238 3.80 - 4.35: 38786 4.35 - 4.90: 67752 Nonbonded interactions: 157073 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.155 3.040 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.183 3.120 nonbonded pdb=" O SER K 92 " pdb=" OG SER K 100 " model vdw 2.184 3.040 nonbonded pdb=" O SER I 92 " pdb=" OG SER I 100 " model vdw 2.200 3.040 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.202 3.040 ... (remaining 157068 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.470 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.010 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.008 0.047 19434 Z= 0.509 Angle : 0.780 7.290 26418 Z= 0.394 Chirality : 0.052 0.343 3153 Planarity : 0.004 0.038 3309 Dihedral : 15.085 115.097 7830 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2352 helix: 2.41 (0.30), residues: 282 sheet: -0.34 (0.18), residues: 771 loop : -0.51 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 153 HIS 0.004 0.001 HIS K 203 PHE 0.019 0.002 PHE I 121 TYR 0.014 0.001 TYR I 178 ARG 0.007 0.001 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.951 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: A 260 MET cc_start: 0.8421 (mmm) cc_final: 0.8187 (mtp) REVERT: A 320 MET cc_start: 0.7235 (ptp) cc_final: 0.7030 (ptp) REVERT: B 67 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7823 (tp30) REVERT: B 77 ILE cc_start: 0.9202 (mm) cc_final: 0.8971 (mp) REVERT: B 86 ASP cc_start: 0.8217 (t0) cc_final: 0.7845 (t0) REVERT: D 67 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7870 (tp30) REVERT: D 74 GLU cc_start: 0.7381 (mp0) cc_final: 0.7037 (mp0) REVERT: F 67 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7595 (tp30) REVERT: F 86 ASP cc_start: 0.8064 (t0) cc_final: 0.7813 (t0) REVERT: F 105 GLN cc_start: 0.8478 (tp40) cc_final: 0.8173 (tp40) REVERT: G 141 LEU cc_start: 0.8417 (mp) cc_final: 0.8107 (mp) REVERT: G 144 PHE cc_start: 0.8354 (p90) cc_final: 0.7902 (p90) REVERT: G 145 TYR cc_start: 0.6973 (t80) cc_final: 0.6652 (t80) REVERT: G 178 TYR cc_start: 0.6600 (m-10) cc_final: 0.6363 (m-10) REVERT: H 164 TRP cc_start: 0.7486 (m100) cc_final: 0.7097 (m100) REVERT: H 205 ILE cc_start: 0.7319 (mp) cc_final: 0.7067 (mp) REVERT: H 210 HIS cc_start: 0.7860 (t-170) cc_final: 0.7333 (t-170) REVERT: H 214 ASN cc_start: 0.7863 (t0) cc_final: 0.7493 (t0) REVERT: H 219 LYS cc_start: 0.7992 (tttm) cc_final: 0.7503 (ttpp) REVERT: I 141 LEU cc_start: 0.8228 (mp) cc_final: 0.7893 (tp) REVERT: I 180 LEU cc_start: 0.8816 (tt) cc_final: 0.8605 (tp) REVERT: J 164 TRP cc_start: 0.7638 (m100) cc_final: 0.6900 (m100) REVERT: J 205 ILE cc_start: 0.7366 (mp) cc_final: 0.6963 (mp) REVERT: J 219 LYS cc_start: 0.7902 (tttm) cc_final: 0.7463 (ttpp) REVERT: K 50 ILE cc_start: 0.9024 (pt) cc_final: 0.8808 (mt) REVERT: K 68 LYS cc_start: 0.8779 (tttt) cc_final: 0.7715 (tptt) REVERT: K 108 LEU cc_start: 0.8969 (mp) cc_final: 0.8431 (tt) REVERT: K 128 GLU cc_start: 0.6997 (mp0) cc_final: 0.6670 (mp0) REVERT: K 150 LYS cc_start: 0.6842 (tppt) cc_final: 0.6412 (tmtt) REVERT: L 132 PHE cc_start: 0.7825 (m-80) cc_final: 0.7435 (m-10) REVERT: L 153 LYS cc_start: 0.7750 (tptm) cc_final: 0.6846 (tptt) REVERT: L 164 TRP cc_start: 0.7412 (m100) cc_final: 0.6513 (m100) REVERT: L 179 VAL cc_start: 0.8917 (t) cc_final: 0.8680 (p) REVERT: L 205 ILE cc_start: 0.7300 (mp) cc_final: 0.6665 (mp) REVERT: L 210 HIS cc_start: 0.7432 (t-170) cc_final: 0.7220 (t-170) REVERT: L 219 LYS cc_start: 0.7904 (tttm) cc_final: 0.7590 (ttpp) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3583 time to fit residues: 220.7588 Evaluate side-chains 277 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN E 197 GLN E 322 ASN G 53 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088823 restraints weight = 33784.834| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.11 r_work: 0.2755 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19434 Z= 0.213 Angle : 0.626 8.470 26418 Z= 0.313 Chirality : 0.048 0.359 3153 Planarity : 0.004 0.045 3309 Dihedral : 10.848 80.001 3573 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 8.24 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2352 helix: 2.63 (0.30), residues: 282 sheet: -0.28 (0.18), residues: 780 loop : -0.54 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 153 HIS 0.004 0.001 HIS E 184 PHE 0.018 0.001 PHE I 123 TYR 0.024 0.001 TYR K 178 ARG 0.004 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 2.209 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: A 35 GLU cc_start: 0.8105 (tt0) cc_final: 0.7218 (tt0) REVERT: A 208 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7585 (ptp-170) REVERT: A 320 MET cc_start: 0.7456 (ptp) cc_final: 0.6983 (ptp) REVERT: A 322 ASN cc_start: 0.6552 (t0) cc_final: 0.6019 (t0) REVERT: B 67 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8247 (tp30) REVERT: B 77 ILE cc_start: 0.9145 (mm) cc_final: 0.8939 (mp) REVERT: B 86 ASP cc_start: 0.8872 (t0) cc_final: 0.8441 (t0) REVERT: C 260 MET cc_start: 0.8886 (mtp) cc_final: 0.8492 (mtp) REVERT: D 67 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8286 (tp30) REVERT: D 74 GLU cc_start: 0.7920 (mp0) cc_final: 0.7396 (mp0) REVERT: F 67 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8055 (tp30) REVERT: F 74 GLU cc_start: 0.7949 (mp0) cc_final: 0.7510 (mp0) REVERT: F 86 ASP cc_start: 0.8912 (t0) cc_final: 0.8524 (t0) REVERT: F 105 GLN cc_start: 0.8669 (tp40) cc_final: 0.8281 (tp40) REVERT: G 141 LEU cc_start: 0.8353 (mp) cc_final: 0.8003 (mp) REVERT: G 144 PHE cc_start: 0.8262 (p90) cc_final: 0.7744 (p90) REVERT: G 145 TYR cc_start: 0.7040 (t80) cc_final: 0.6702 (t80) REVERT: H 89 ASP cc_start: 0.8845 (p0) cc_final: 0.8103 (p0) REVERT: H 164 TRP cc_start: 0.7564 (m100) cc_final: 0.7310 (m100) REVERT: H 205 ILE cc_start: 0.7476 (mp) cc_final: 0.7102 (mp) REVERT: H 210 HIS cc_start: 0.7082 (t-170) cc_final: 0.6730 (t-170) REVERT: H 214 ASN cc_start: 0.8131 (t0) cc_final: 0.7880 (t0) REVERT: I 87 ASP cc_start: 0.8450 (t0) cc_final: 0.8136 (t0) REVERT: I 141 LEU cc_start: 0.7957 (mp) cc_final: 0.7701 (tp) REVERT: I 204 GLN cc_start: 0.8095 (mt0) cc_final: 0.7769 (mp10) REVERT: J 83 MET cc_start: 0.8223 (mtp) cc_final: 0.7953 (mtp) REVERT: J 90 ASP cc_start: 0.8967 (m-30) cc_final: 0.8717 (m-30) REVERT: J 164 TRP cc_start: 0.7656 (m100) cc_final: 0.6932 (m100) REVERT: J 205 ILE cc_start: 0.7213 (mp) cc_final: 0.6641 (mm) REVERT: J 210 HIS cc_start: 0.6918 (t-170) cc_final: 0.6676 (t-170) REVERT: K 107 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8497 (mtmm) REVERT: K 108 LEU cc_start: 0.9002 (mp) cc_final: 0.8653 (tt) REVERT: K 128 GLU cc_start: 0.7212 (mp0) cc_final: 0.6872 (mp0) REVERT: K 141 LEU cc_start: 0.8170 (mp) cc_final: 0.7707 (tp) REVERT: K 153 TRP cc_start: 0.4528 (t-100) cc_final: 0.4301 (t-100) REVERT: L 46 GLU cc_start: 0.8275 (tt0) cc_final: 0.8054 (tt0) REVERT: L 83 MET cc_start: 0.8102 (mtp) cc_final: 0.7894 (ttm) REVERT: L 132 PHE cc_start: 0.7919 (m-80) cc_final: 0.7685 (m-10) REVERT: L 164 TRP cc_start: 0.7504 (m100) cc_final: 0.6099 (m100) REVERT: L 179 VAL cc_start: 0.8895 (t) cc_final: 0.8666 (p) REVERT: L 205 ILE cc_start: 0.7507 (mp) cc_final: 0.6981 (mm) outliers start: 25 outliers final: 17 residues processed: 342 average time/residue: 0.3129 time to fit residues: 163.2517 Evaluate side-chains 300 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0304 > 50: distance: 59 - 188: 11.166 distance: 123 - 124: 9.383 distance: 124 - 125: 10.194 distance: 124 - 127: 9.796 distance: 125 - 126: 8.846 distance: 125 - 130: 4.604 distance: 127 - 128: 5.691 distance: 127 - 129: 3.985 distance: 130 - 131: 4.617 distance: 131 - 132: 7.452 distance: 132 - 133: 18.201 distance: 132 - 138: 9.090 distance: 134 - 135: 6.989 distance: 135 - 136: 5.567 distance: 135 - 137: 4.992 distance: 139 - 140: 6.307 distance: 139 - 142: 5.764 distance: 140 - 141: 4.044 distance: 140 - 147: 5.326 distance: 142 - 143: 3.596 distance: 143 - 144: 4.348 distance: 145 - 146: 3.025 distance: 147 - 148: 4.135 distance: 148 - 149: 7.313 distance: 149 - 150: 9.436 distance: 152 - 154: 5.548 distance: 155 - 156: 4.815 distance: 156 - 157: 6.035 distance: 156 - 159: 4.350 distance: 157 - 158: 14.897 distance: 157 - 162: 9.513 distance: 159 - 160: 10.665 distance: 159 - 161: 6.060 distance: 162 - 163: 9.845 distance: 163 - 164: 19.876 distance: 163 - 166: 12.647 distance: 164 - 165: 16.695 distance: 164 - 174: 16.971 distance: 166 - 167: 4.652 distance: 167 - 168: 4.197 distance: 167 - 169: 4.424 distance: 168 - 170: 3.214 distance: 169 - 171: 3.887 distance: 174 - 175: 7.854 distance: 174 - 230: 4.700 distance: 175 - 176: 15.091 distance: 176 - 177: 13.700 distance: 176 - 178: 24.952 distance: 178 - 179: 16.944 distance: 179 - 180: 19.682 distance: 179 - 182: 19.119 distance: 180 - 181: 25.505 distance: 180 - 183: 9.355 distance: 183 - 184: 11.867 distance: 184 - 185: 17.816 distance: 184 - 187: 15.071 distance: 185 - 186: 13.921 distance: 185 - 189: 5.189 distance: 187 - 188: 19.181 distance: 189 - 190: 17.181 distance: 189 - 195: 8.681 distance: 190 - 193: 7.110 distance: 191 - 192: 16.499 distance: 191 - 196: 14.496 distance: 193 - 194: 9.018 distance: 194 - 195: 15.470