Starting phenix.real_space_refine on Sun Aug 24 17:11:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3a_22654/08_2025/7k3a_22654.cif" } resolution = 4.2 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= 0.005 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 99 5.16 5 C 13359 2.51 5 N 3618 2.21 5 O 4350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 21426 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.84, per 1000 atoms: 0.27 Number of scatterers: 21426 At special positions: 0 Unit cell: (183.54, 183.54, 144.97, 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 99 16.00 O 4350 8.00 N 3618 7.00 C 13359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.32 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=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.83 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=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.93 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=2.02 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 F 144 " - pdb=" SG CYS F 148 " distance=2.03 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 B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " 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: 1.88 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 19.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (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 38 through 50 removed outlier: 4.322A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (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 38 through 50 removed outlier: 4.323A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (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 38 through 50 removed outlier: 4.322A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 172 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 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: 3.517A 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 197 through 202 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix 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: 3.516A 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 197 through 202 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 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: 3.516A 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 197 through 202 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.830A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.553A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.135A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.555A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.134A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.554A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.193A 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 23 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.659A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.057A 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: 4.135A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (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 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.164A 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: 6.090A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.372A 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: 3.557A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.823A 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 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.163A 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: 6.090A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER J 187 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA J 178 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER J 189 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.607A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.978A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.883A 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 159 removed outlier: 3.999A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (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 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.164A 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: 6.091A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 187 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA L 178 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER L 189 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 160 through 164 921 hydrogen bonds defined for protein. 2346 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: 3.26 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6898 1.35 - 1.47: 5629 1.47 - 1.60: 9205 1.60 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 21870 Sorted by residual: bond pdb=" C1 MAN U 4 " pdb=" C2 MAN U 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 21865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 28328 1.72 - 3.44: 1141 3.44 - 5.16: 166 5.16 - 6.87: 55 6.87 - 8.59: 10 Bond angle restraints: 29700 Sorted by residual: angle pdb=" CA VAL J 194 " pdb=" C VAL J 194 " pdb=" N PRO J 195 " ideal model delta sigma weight residual 116.57 120.04 -3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" CA VAL L 194 " pdb=" C VAL L 194 " pdb=" N PRO L 195 " ideal model delta sigma weight residual 116.57 120.01 -3.44 9.80e-01 1.04e+00 1.23e+01 angle pdb=" CA VAL H 194 " pdb=" C VAL H 194 " pdb=" N PRO H 195 " ideal model delta sigma weight residual 116.57 119.98 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" C VAL J 194 " pdb=" CA VAL J 194 " pdb=" CB VAL J 194 " ideal model delta sigma weight residual 109.33 112.39 -3.06 9.80e-01 1.04e+00 9.78e+00 angle pdb=" C VAL H 194 " pdb=" CA VAL H 194 " pdb=" CB VAL H 194 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.68e+00 ... (remaining 29695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 12868 21.98 - 43.97: 734 43.97 - 65.95: 102 65.95 - 87.93: 48 87.93 - 109.91: 24 Dihedral angle restraints: 13776 sinusoidal: 6069 harmonic: 7707 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 42.08 50.92 1 1.00e+01 1.00e-02 3.55e+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 47.87 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual -73.00 -0.71 -72.29 1 2.00e+01 2.50e-03 1.67e+01 ... (remaining 13773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3051 0.079 - 0.159: 394 0.159 - 0.238: 23 0.238 - 0.317: 15 0.317 - 0.397: 3 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 3483 not shown) Planarity restraints: 3771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 178 " -0.006 2.00e-02 2.50e+03 1.40e-02 3.90e+00 pdb=" CG TYR I 178 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR I 178 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR I 178 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR I 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR I 178 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 178 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 220 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO A 221 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 220 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 221 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.021 5.00e-02 4.00e+02 ... (remaining 3768 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 316 2.62 - 3.19: 18968 3.19 - 3.76: 33629 3.76 - 4.33: 48357 4.33 - 4.90: 78252 Nonbonded interactions: 179522 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.053 3.040 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.124 3.120 nonbonded pdb=" O GLY K 24 " pdb=" OG1 THR K 71 " model vdw 2.128 3.040 nonbonded pdb=" OE1 GLN C 210 " pdb=" NE ARG E 220 " model vdw 2.145 3.120 nonbonded pdb=" O TYR I 191 " pdb=" OH TYR I 197 " model vdw 2.164 3.040 ... (remaining 179517 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: 0.04 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.040 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 19.780 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.005 0.293 21954 Z= 0.243 Angle : 0.860 18.087 29922 Z= 0.432 Chirality : 0.054 0.397 3486 Planarity : 0.005 0.038 3753 Dihedral : 14.882 109.914 8754 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.17 % Allowed : 0.60 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.62 (0.16), residues: 2649 helix: 1.75 (0.26), residues: 384 sheet: -0.20 (0.17), residues: 867 loop : -1.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 17 TYR 0.030 0.002 TYR I 178 PHE 0.019 0.002 PHE I 123 TRP 0.022 0.002 TRP H 50 HIS 0.006 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00430 (21870) covalent geometry : angle 0.81782 (29700) SS BOND : bond 0.06712 ( 30) SS BOND : angle 2.86381 ( 60) hydrogen bonds : bond 0.15341 ( 879) hydrogen bonds : angle 7.11670 ( 2346) link_ALPHA1-2 : bond 0.01334 ( 3) link_ALPHA1-2 : angle 2.44007 ( 9) link_ALPHA1-3 : bond 0.00849 ( 9) link_ALPHA1-3 : angle 4.32139 ( 27) link_ALPHA1-6 : bond 0.00952 ( 9) link_ALPHA1-6 : angle 4.11344 ( 27) link_BETA1-4 : bond 0.00497 ( 15) link_BETA1-4 : angle 2.09966 ( 45) link_NAG-ASN : bond 0.00423 ( 18) link_NAG-ASN : angle 3.24360 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 498 time to evaluate : 0.820 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: A 168 MET cc_start: 0.7617 (mmm) cc_final: 0.5948 (mmt) REVERT: A 233 TYR cc_start: 0.7243 (m-80) cc_final: 0.7013 (m-10) REVERT: B 73 VAL cc_start: 0.9090 (t) cc_final: 0.8772 (t) REVERT: B 80 LEU cc_start: 0.9427 (tp) cc_final: 0.8351 (tt) REVERT: C 316 LEU cc_start: 0.7963 (tp) cc_final: 0.7717 (tt) REVERT: D 81 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7577 (mt-10) REVERT: D 89 ILE cc_start: 0.9117 (mt) cc_final: 0.7105 (mt) REVERT: D 94 TYR cc_start: 0.7837 (t80) cc_final: 0.7512 (t80) REVERT: D 95 ASN cc_start: 0.8553 (m-40) cc_final: 0.8220 (m110) REVERT: F 80 LEU cc_start: 0.9427 (tp) cc_final: 0.9200 (tp) REVERT: G 143 ASN cc_start: 0.8240 (m110) cc_final: 0.7736 (p0) REVERT: G 159 LEU cc_start: 0.7708 (tp) cc_final: 0.7461 (tt) REVERT: H 121 MET cc_start: 0.8576 (tpt) cc_final: 0.8124 (tpt) REVERT: I 191 TYR cc_start: 0.7706 (t80) cc_final: 0.7487 (t80) REVERT: J 98 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7866 (ttp-170) REVERT: J 164 TRP cc_start: 0.6005 (m100) cc_final: 0.5792 (m100) REVERT: K 174 LYS cc_start: 0.7940 (pttt) cc_final: 0.7654 (tptp) REVERT: K 195 LYS cc_start: 0.8906 (mptt) cc_final: 0.8690 (pttp) REVERT: L 81 MET cc_start: 0.7535 (ttp) cc_final: 0.7312 (tmm) outliers start: 4 outliers final: 0 residues processed: 502 average time/residue: 0.1786 time to fit residues: 126.5255 Evaluate side-chains 202 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS F 106 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 142 ASN G 143 ASN H 57 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037830 restraints weight = 180075.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038872 restraints weight = 107762.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.039589 restraints weight = 75750.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040062 restraints weight = 58955.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.040357 restraints weight = 49643.769| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21954 Z= 0.205 Angle : 0.734 9.655 29922 Z= 0.365 Chirality : 0.049 0.321 3486 Planarity : 0.006 0.092 3753 Dihedral : 10.633 79.016 3960 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.50 (0.16), residues: 2649 helix: 2.02 (0.25), residues: 375 sheet: -0.01 (0.17), residues: 807 loop : -1.18 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 127 TYR 0.020 0.002 TYR C 233 PHE 0.035 0.002 PHE F 171 TRP 0.014 0.002 TRP H 50 HIS 0.011 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00439 (21870) covalent geometry : angle 0.70860 (29700) SS BOND : bond 0.00346 ( 30) SS BOND : angle 0.94781 ( 60) hydrogen bonds : bond 0.03916 ( 879) hydrogen bonds : angle 5.95339 ( 2346) link_ALPHA1-2 : bond 0.00946 ( 3) link_ALPHA1-2 : angle 1.50137 ( 9) link_ALPHA1-3 : bond 0.00541 ( 9) link_ALPHA1-3 : angle 2.96075 ( 27) link_ALPHA1-6 : bond 0.01026 ( 9) link_ALPHA1-6 : angle 3.34208 ( 27) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 2.22215 ( 45) link_NAG-ASN : bond 0.00528 ( 18) link_NAG-ASN : angle 2.60755 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.625 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: A 32 ASP cc_start: 0.8683 (p0) cc_final: 0.8444 (m-30) REVERT: A 82 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8591 (mm-30) REVERT: B 73 VAL cc_start: 0.9446 (t) cc_final: 0.8647 (t) REVERT: B 76 ARG cc_start: 0.8102 (ttt-90) cc_final: 0.7829 (ttt-90) REVERT: B 139 LYS cc_start: 0.8543 (tppt) cc_final: 0.8306 (tppp) REVERT: D 78 GLN cc_start: 0.8215 (tt0) cc_final: 0.7907 (tm-30) REVERT: D 83 TYR cc_start: 0.8879 (t80) cc_final: 0.8610 (t80) REVERT: D 95 ASN cc_start: 0.9167 (m-40) cc_final: 0.8900 (m-40) REVERT: E 18 HIS cc_start: 0.8459 (p-80) cc_final: 0.7236 (p-80) REVERT: E 27 LYS cc_start: 0.8511 (ptmm) cc_final: 0.8076 (mptt) REVERT: E 190 GLU cc_start: 0.9184 (tt0) cc_final: 0.8888 (tt0) REVERT: F 9 PHE cc_start: 0.8381 (p90) cc_final: 0.8057 (p90) REVERT: F 21 TRP cc_start: 0.9251 (m100) cc_final: 0.8833 (m100) REVERT: F 163 ARG cc_start: 0.7105 (ttt90) cc_final: 0.6859 (mtm180) REVERT: G 143 ASN cc_start: 0.8826 (m-40) cc_final: 0.7899 (p0) REVERT: G 159 LEU cc_start: 0.8078 (tp) cc_final: 0.7858 (tt) REVERT: G 191 TYR cc_start: 0.8580 (t80) cc_final: 0.8371 (t80) REVERT: G 197 TYR cc_start: 0.8398 (m-10) cc_final: 0.7943 (m-80) REVERT: H 81 MET cc_start: 0.8275 (tmm) cc_final: 0.8058 (tmm) REVERT: I 191 TYR cc_start: 0.8096 (t80) cc_final: 0.7619 (t80) REVERT: I 193 LYS cc_start: 0.9533 (ptmt) cc_final: 0.9304 (ptmm) REVERT: J 98 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8092 (ttp-170) REVERT: J 106 MET cc_start: 0.8813 (mtm) cc_final: 0.8577 (mtm) REVERT: J 121 MET cc_start: 0.9231 (tpt) cc_final: 0.8751 (tpt) REVERT: J 164 TRP cc_start: 0.6563 (m100) cc_final: 0.5988 (m100) REVERT: K 174 LYS cc_start: 0.8249 (pttt) cc_final: 0.7805 (tptp) REVERT: L 81 MET cc_start: 0.8730 (ttp) cc_final: 0.8060 (tmm) REVERT: L 121 MET cc_start: 0.9230 (tpt) cc_final: 0.8715 (tpt) REVERT: L 148 LEU cc_start: 0.7739 (mt) cc_final: 0.7371 (pt) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.1589 time to fit residues: 65.9157 Evaluate side-chains 184 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 152 GLN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.046542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035988 restraints weight = 188698.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036929 restraints weight = 113219.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.037566 restraints weight = 80522.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037994 restraints weight = 63588.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.038276 restraints weight = 54087.298| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21954 Z= 0.275 Angle : 0.778 10.107 29922 Z= 0.387 Chirality : 0.049 0.293 3486 Planarity : 0.006 0.058 3753 Dihedral : 10.097 73.771 3960 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.80 (0.16), residues: 2649 helix: 1.01 (0.25), residues: 402 sheet: -0.01 (0.17), residues: 819 loop : -1.32 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 123 TYR 0.022 0.002 TYR E 257 PHE 0.021 0.002 PHE L 176 TRP 0.020 0.002 TRP E 84 HIS 0.011 0.002 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00580 (21870) covalent geometry : angle 0.75623 (29700) SS BOND : bond 0.00482 ( 30) SS BOND : angle 1.08412 ( 60) hydrogen bonds : bond 0.04018 ( 879) hydrogen bonds : angle 5.98376 ( 2346) link_ALPHA1-2 : bond 0.01058 ( 3) link_ALPHA1-2 : angle 1.20019 ( 9) link_ALPHA1-3 : bond 0.00479 ( 9) link_ALPHA1-3 : angle 2.79120 ( 27) link_ALPHA1-6 : bond 0.00854 ( 9) link_ALPHA1-6 : angle 3.19833 ( 27) link_BETA1-4 : bond 0.00420 ( 15) link_BETA1-4 : angle 1.82452 ( 45) link_NAG-ASN : bond 0.00640 ( 18) link_NAG-ASN : angle 2.71292 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.504 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: A 18 HIS cc_start: 0.8016 (p-80) cc_final: 0.7807 (p-80) REVERT: C 32 ASP cc_start: 0.8961 (p0) cc_final: 0.8632 (m-30) REVERT: C 33 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8149 (mm-40) REVERT: C 168 MET cc_start: 0.8318 (tpp) cc_final: 0.8036 (tpp) REVERT: C 268 MET cc_start: 0.8531 (ttm) cc_final: 0.8324 (ttm) REVERT: D 83 TYR cc_start: 0.8896 (t80) cc_final: 0.8679 (t80) REVERT: E 27 LYS cc_start: 0.8589 (ptmm) cc_final: 0.8085 (mptt) REVERT: E 32 ASP cc_start: 0.8827 (m-30) cc_final: 0.8420 (p0) REVERT: G 148 GLU cc_start: 0.8439 (pm20) cc_final: 0.8030 (pm20) REVERT: G 197 TYR cc_start: 0.8414 (m-10) cc_final: 0.7960 (m-80) REVERT: H 81 MET cc_start: 0.8468 (tmm) cc_final: 0.8224 (tmm) REVERT: I 143 ASN cc_start: 0.8544 (m-40) cc_final: 0.7385 (p0) REVERT: I 191 TYR cc_start: 0.8112 (t80) cc_final: 0.7611 (t80) REVERT: J 81 MET cc_start: 0.8504 (tmm) cc_final: 0.8234 (tmm) REVERT: J 106 MET cc_start: 0.8893 (mtm) cc_final: 0.8648 (mtm) REVERT: J 121 MET cc_start: 0.9256 (tpt) cc_final: 0.8905 (tpt) REVERT: K 143 ASN cc_start: 0.8632 (m-40) cc_final: 0.7529 (p0) REVERT: K 174 LYS cc_start: 0.8213 (pttt) cc_final: 0.7782 (tptp) REVERT: L 10 GLU cc_start: 0.8669 (tp30) cc_final: 0.8318 (tm-30) REVERT: L 81 MET cc_start: 0.8536 (ttp) cc_final: 0.7964 (tmm) REVERT: L 121 MET cc_start: 0.9237 (tpt) cc_final: 0.8696 (tpt) REVERT: L 148 LEU cc_start: 0.7838 (mt) cc_final: 0.7358 (pt) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.1617 time to fit residues: 55.0979 Evaluate side-chains 153 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 6 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 161 optimal weight: 0.1980 chunk 245 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN G 6 GLN G 40 GLN G 129 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.047382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036692 restraints weight = 185148.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037696 restraints weight = 108982.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.038383 restraints weight = 76334.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.038812 restraints weight = 59575.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039119 restraints weight = 50592.838| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21954 Z= 0.164 Angle : 0.668 9.744 29922 Z= 0.331 Chirality : 0.048 0.297 3486 Planarity : 0.005 0.050 3753 Dihedral : 9.067 67.383 3960 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.66 (0.16), residues: 2649 helix: 1.17 (0.25), residues: 402 sheet: 0.03 (0.18), residues: 807 loop : -1.20 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 17 TYR 0.024 0.002 TYR K 191 PHE 0.025 0.002 PHE L 176 TRP 0.010 0.001 TRP L 47 HIS 0.008 0.001 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00350 (21870) covalent geometry : angle 0.64628 (29700) SS BOND : bond 0.00350 ( 30) SS BOND : angle 0.84292 ( 60) hydrogen bonds : bond 0.03511 ( 879) hydrogen bonds : angle 5.67349 ( 2346) link_ALPHA1-2 : bond 0.00953 ( 3) link_ALPHA1-2 : angle 1.23092 ( 9) link_ALPHA1-3 : bond 0.00467 ( 9) link_ALPHA1-3 : angle 2.95821 ( 27) link_ALPHA1-6 : bond 0.00471 ( 9) link_ALPHA1-6 : angle 2.71692 ( 27) link_BETA1-4 : bond 0.00265 ( 15) link_BETA1-4 : angle 1.69245 ( 45) link_NAG-ASN : bond 0.00548 ( 18) link_NAG-ASN : angle 2.51974 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.832 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: A 18 HIS cc_start: 0.8098 (p-80) cc_final: 0.7849 (p-80) REVERT: B 9 PHE cc_start: 0.8544 (p90) cc_final: 0.8295 (p90) REVERT: B 100 VAL cc_start: 0.9713 (t) cc_final: 0.9422 (t) REVERT: B 133 MET cc_start: 0.6262 (mtm) cc_final: 0.5865 (mmm) REVERT: C 233 TYR cc_start: 0.8211 (m-10) cc_final: 0.7670 (m-10) REVERT: C 268 MET cc_start: 0.8554 (ttm) cc_final: 0.8310 (ttt) REVERT: D 83 TYR cc_start: 0.8855 (t80) cc_final: 0.8626 (t80) REVERT: E 18 HIS cc_start: 0.8325 (p-80) cc_final: 0.7987 (p-80) REVERT: E 27 LYS cc_start: 0.8682 (ptmm) cc_final: 0.8259 (mptt) REVERT: F 76 ARG cc_start: 0.8239 (ttt180) cc_final: 0.7974 (ttt180) REVERT: F 162 TYR cc_start: 0.7677 (m-80) cc_final: 0.7428 (m-80) REVERT: G 191 TYR cc_start: 0.8612 (t80) cc_final: 0.8395 (t80) REVERT: G 197 TYR cc_start: 0.8381 (m-10) cc_final: 0.7900 (m-80) REVERT: H 81 MET cc_start: 0.8479 (tmm) cc_final: 0.8252 (tmm) REVERT: H 106 MET cc_start: 0.8762 (mtm) cc_final: 0.8532 (mtm) REVERT: H 121 MET cc_start: 0.9045 (tpt) cc_final: 0.8324 (tpt) REVERT: I 191 TYR cc_start: 0.7979 (t80) cc_final: 0.7596 (t80) REVERT: J 10 GLU cc_start: 0.8811 (tp30) cc_final: 0.7940 (tm-30) REVERT: J 106 MET cc_start: 0.8894 (mtm) cc_final: 0.8632 (mtm) REVERT: J 121 MET cc_start: 0.9234 (tpt) cc_final: 0.8892 (tpt) REVERT: J 164 TRP cc_start: 0.6432 (m100) cc_final: 0.5876 (m100) REVERT: K 143 ASN cc_start: 0.8503 (m-40) cc_final: 0.7528 (p0) REVERT: K 174 LYS cc_start: 0.8250 (pttt) cc_final: 0.7768 (tptp) REVERT: L 10 GLU cc_start: 0.8610 (tp30) cc_final: 0.8299 (tm-30) REVERT: L 121 MET cc_start: 0.9222 (tpt) cc_final: 0.8658 (tpt) outliers start: 3 outliers final: 0 residues processed: 243 average time/residue: 0.1515 time to fit residues: 54.7969 Evaluate side-chains 159 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 0.2980 chunk 176 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 231 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.047698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037017 restraints weight = 183802.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038041 restraints weight = 108114.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.038702 restraints weight = 75687.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039165 restraints weight = 59416.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039448 restraints weight = 50240.755| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21954 Z= 0.136 Angle : 0.643 9.669 29922 Z= 0.316 Chirality : 0.048 0.414 3486 Planarity : 0.005 0.087 3753 Dihedral : 8.381 62.449 3960 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.52 (0.16), residues: 2649 helix: 1.28 (0.25), residues: 402 sheet: -0.02 (0.17), residues: 870 loop : -1.05 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 127 TYR 0.024 0.002 TYR K 191 PHE 0.026 0.001 PHE L 176 TRP 0.012 0.001 TRP K 153 HIS 0.007 0.001 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00294 (21870) covalent geometry : angle 0.62268 (29700) SS BOND : bond 0.00394 ( 30) SS BOND : angle 0.77707 ( 60) hydrogen bonds : bond 0.03362 ( 879) hydrogen bonds : angle 5.53074 ( 2346) link_ALPHA1-2 : bond 0.00872 ( 3) link_ALPHA1-2 : angle 1.26358 ( 9) link_ALPHA1-3 : bond 0.00605 ( 9) link_ALPHA1-3 : angle 2.89691 ( 27) link_ALPHA1-6 : bond 0.00442 ( 9) link_ALPHA1-6 : angle 2.46089 ( 27) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 1.56280 ( 45) link_NAG-ASN : bond 0.00649 ( 18) link_NAG-ASN : angle 2.39163 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.774 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 320 MET cc_start: 0.7810 (ptp) cc_final: 0.7372 (ptt) REVERT: B 38 LEU cc_start: 0.8596 (mm) cc_final: 0.8388 (mm) REVERT: B 42 GLN cc_start: 0.9015 (pm20) cc_final: 0.8623 (pm20) REVERT: B 100 VAL cc_start: 0.9715 (t) cc_final: 0.9468 (t) REVERT: B 103 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8652 (mm-30) REVERT: B 118 LEU cc_start: 0.9493 (tt) cc_final: 0.9224 (pp) REVERT: C 268 MET cc_start: 0.8559 (ttm) cc_final: 0.8330 (ttt) REVERT: D 83 TYR cc_start: 0.8807 (t80) cc_final: 0.8596 (t80) REVERT: E 18 HIS cc_start: 0.8247 (p-80) cc_final: 0.7836 (p-80) REVERT: E 27 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8250 (mptt) REVERT: F 76 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8145 (ttt180) REVERT: G 148 GLU cc_start: 0.8394 (pm20) cc_final: 0.7580 (pm20) REVERT: G 191 TYR cc_start: 0.8636 (t80) cc_final: 0.8300 (t80) REVERT: G 197 TYR cc_start: 0.8379 (m-10) cc_final: 0.7883 (m-80) REVERT: H 121 MET cc_start: 0.9072 (tpt) cc_final: 0.8417 (tpt) REVERT: I 191 TYR cc_start: 0.7921 (t80) cc_final: 0.7454 (t80) REVERT: J 10 GLU cc_start: 0.8741 (tp30) cc_final: 0.7968 (tm-30) REVERT: J 81 MET cc_start: 0.8436 (tmm) cc_final: 0.8132 (tmm) REVERT: J 106 MET cc_start: 0.8975 (mtm) cc_final: 0.8636 (mtm) REVERT: J 121 MET cc_start: 0.9225 (tpt) cc_final: 0.8869 (tpt) REVERT: J 164 TRP cc_start: 0.6387 (m100) cc_final: 0.5837 (m100) REVERT: K 174 LYS cc_start: 0.8232 (pttt) cc_final: 0.7773 (tptp) REVERT: L 121 MET cc_start: 0.9187 (tpt) cc_final: 0.8607 (tpt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1440 time to fit residues: 49.0673 Evaluate side-chains 161 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 94 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 228 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS G 6 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN K 143 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.035875 restraints weight = 186704.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036819 restraints weight = 112121.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037451 restraints weight = 79564.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037876 restraints weight = 62697.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038140 restraints weight = 53238.191| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21954 Z= 0.203 Angle : 0.683 10.565 29922 Z= 0.337 Chirality : 0.047 0.304 3486 Planarity : 0.005 0.048 3753 Dihedral : 8.129 57.270 3960 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.64 (0.16), residues: 2649 helix: 1.11 (0.25), residues: 402 sheet: 0.04 (0.18), residues: 807 loop : -1.15 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 38 TYR 0.023 0.002 TYR K 191 PHE 0.024 0.002 PHE L 176 TRP 0.011 0.002 TRP J 36 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00437 (21870) covalent geometry : angle 0.66156 (29700) SS BOND : bond 0.00409 ( 30) SS BOND : angle 1.01493 ( 60) hydrogen bonds : bond 0.03517 ( 879) hydrogen bonds : angle 5.61416 ( 2346) link_ALPHA1-2 : bond 0.00973 ( 3) link_ALPHA1-2 : angle 1.17572 ( 9) link_ALPHA1-3 : bond 0.00483 ( 9) link_ALPHA1-3 : angle 2.85882 ( 27) link_ALPHA1-6 : bond 0.00529 ( 9) link_ALPHA1-6 : angle 2.78092 ( 27) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.57499 ( 45) link_NAG-ASN : bond 0.00610 ( 18) link_NAG-ASN : angle 2.46882 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.541 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 18 HIS cc_start: 0.8223 (p-80) cc_final: 0.7916 (p-80) REVERT: A 233 TYR cc_start: 0.8381 (m-10) cc_final: 0.8144 (m-10) REVERT: B 9 PHE cc_start: 0.8575 (p90) cc_final: 0.8314 (p90) REVERT: B 62 LYS cc_start: 0.8850 (mttp) cc_final: 0.8422 (mppt) REVERT: B 100 VAL cc_start: 0.9709 (t) cc_final: 0.9353 (t) REVERT: C 168 MET cc_start: 0.8660 (tpp) cc_final: 0.8335 (tpp) REVERT: C 268 MET cc_start: 0.8540 (ttm) cc_final: 0.8323 (ttt) REVERT: D 83 TYR cc_start: 0.8848 (t80) cc_final: 0.8626 (t80) REVERT: E 18 HIS cc_start: 0.8346 (p-80) cc_final: 0.7952 (p-80) REVERT: E 27 LYS cc_start: 0.8675 (ptmm) cc_final: 0.8189 (mptt) REVERT: G 143 ASN cc_start: 0.8414 (m-40) cc_final: 0.7583 (p0) REVERT: G 148 GLU cc_start: 0.8327 (pm20) cc_final: 0.8072 (pm20) REVERT: G 191 TYR cc_start: 0.8680 (t80) cc_final: 0.8386 (t80) REVERT: G 197 TYR cc_start: 0.8411 (m-10) cc_final: 0.7912 (m-80) REVERT: H 121 MET cc_start: 0.9100 (tpt) cc_final: 0.8460 (tpt) REVERT: I 191 TYR cc_start: 0.7921 (t80) cc_final: 0.7482 (t80) REVERT: J 10 GLU cc_start: 0.8697 (tp30) cc_final: 0.7952 (tm-30) REVERT: J 81 MET cc_start: 0.8472 (tmm) cc_final: 0.8210 (tmm) REVERT: J 106 MET cc_start: 0.8941 (mtm) cc_final: 0.8638 (mtm) REVERT: J 121 MET cc_start: 0.9234 (tpt) cc_final: 0.8896 (tpt) REVERT: J 164 TRP cc_start: 0.6519 (m100) cc_final: 0.5928 (m100) REVERT: K 174 LYS cc_start: 0.8134 (pttt) cc_final: 0.7721 (tptp) REVERT: L 121 MET cc_start: 0.9194 (tpt) cc_final: 0.8585 (tpt) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1516 time to fit residues: 48.9280 Evaluate side-chains 152 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 38 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 131 optimal weight: 0.0670 chunk 124 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 40 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035905 restraints weight = 184781.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036876 restraints weight = 109801.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037542 restraints weight = 77202.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.037980 restraints weight = 60212.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038254 restraints weight = 50797.588| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21954 Z= 0.176 Angle : 0.658 11.451 29922 Z= 0.324 Chirality : 0.047 0.300 3486 Planarity : 0.005 0.046 3753 Dihedral : 7.772 56.382 3960 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.04 % Allowed : 0.90 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.57 (0.16), residues: 2649 helix: 1.19 (0.25), residues: 402 sheet: 0.05 (0.18), residues: 822 loop : -1.11 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 123 TYR 0.020 0.002 TYR K 197 PHE 0.023 0.002 PHE L 176 TRP 0.009 0.001 TRP L 47 HIS 0.007 0.001 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00376 (21870) covalent geometry : angle 0.63767 (29700) SS BOND : bond 0.00437 ( 30) SS BOND : angle 0.95033 ( 60) hydrogen bonds : bond 0.03398 ( 879) hydrogen bonds : angle 5.49143 ( 2346) link_ALPHA1-2 : bond 0.00938 ( 3) link_ALPHA1-2 : angle 1.13780 ( 9) link_ALPHA1-3 : bond 0.00522 ( 9) link_ALPHA1-3 : angle 2.81289 ( 27) link_ALPHA1-6 : bond 0.00526 ( 9) link_ALPHA1-6 : angle 2.60265 ( 27) link_BETA1-4 : bond 0.00256 ( 15) link_BETA1-4 : angle 1.43812 ( 45) link_NAG-ASN : bond 0.00563 ( 18) link_NAG-ASN : angle 2.46107 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.681 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: B 62 LYS cc_start: 0.8796 (mttp) cc_final: 0.8302 (mppt) REVERT: B 100 VAL cc_start: 0.9706 (t) cc_final: 0.9355 (t) REVERT: B 103 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8889 (tp30) REVERT: B 118 LEU cc_start: 0.9514 (tt) cc_final: 0.9240 (pp) REVERT: C 27 LYS cc_start: 0.7398 (mptt) cc_final: 0.7138 (mptt) REVERT: C 268 MET cc_start: 0.8588 (ttm) cc_final: 0.8350 (ttt) REVERT: D 83 TYR cc_start: 0.8824 (t80) cc_final: 0.8571 (t80) REVERT: E 18 HIS cc_start: 0.8264 (p-80) cc_final: 0.7873 (p-80) REVERT: E 27 LYS cc_start: 0.8733 (ptmm) cc_final: 0.8470 (ptmm) REVERT: G 143 ASN cc_start: 0.8394 (m-40) cc_final: 0.7504 (p0) REVERT: G 148 GLU cc_start: 0.8364 (pm20) cc_final: 0.8112 (pm20) REVERT: G 191 TYR cc_start: 0.8776 (t80) cc_final: 0.8442 (t80) REVERT: G 197 TYR cc_start: 0.8413 (m-10) cc_final: 0.7937 (m-80) REVERT: H 121 MET cc_start: 0.9099 (tpt) cc_final: 0.8474 (tpt) REVERT: I 191 TYR cc_start: 0.7910 (t80) cc_final: 0.7468 (t80) REVERT: J 10 GLU cc_start: 0.8668 (tp30) cc_final: 0.8003 (tm-30) REVERT: J 81 MET cc_start: 0.8468 (tmm) cc_final: 0.8232 (tmm) REVERT: J 106 MET cc_start: 0.8936 (mtm) cc_final: 0.8629 (mtm) REVERT: J 121 MET cc_start: 0.9229 (tpt) cc_final: 0.8890 (tpt) REVERT: J 164 TRP cc_start: 0.6601 (m100) cc_final: 0.5965 (m100) REVERT: K 174 LYS cc_start: 0.8187 (pttt) cc_final: 0.7793 (tptp) REVERT: L 121 MET cc_start: 0.9193 (tpt) cc_final: 0.8604 (tpt) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1462 time to fit residues: 46.7816 Evaluate side-chains 150 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 0.3980 chunk 233 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.036820 restraints weight = 181833.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037815 restraints weight = 107961.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038491 restraints weight = 75610.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038949 restraints weight = 59082.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039235 restraints weight = 49753.992| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21954 Z= 0.116 Angle : 0.626 11.671 29922 Z= 0.306 Chirality : 0.047 0.308 3486 Planarity : 0.004 0.044 3753 Dihedral : 7.525 58.322 3960 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.42 (0.16), residues: 2649 helix: 1.46 (0.25), residues: 402 sheet: 0.13 (0.18), residues: 843 loop : -1.06 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 123 TYR 0.021 0.001 TYR C 233 PHE 0.023 0.002 PHE E 294 TRP 0.027 0.001 TRP E 222 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00251 (21870) covalent geometry : angle 0.60618 (29700) SS BOND : bond 0.00309 ( 30) SS BOND : angle 0.81084 ( 60) hydrogen bonds : bond 0.03230 ( 879) hydrogen bonds : angle 5.27829 ( 2346) link_ALPHA1-2 : bond 0.00831 ( 3) link_ALPHA1-2 : angle 1.27429 ( 9) link_ALPHA1-3 : bond 0.00652 ( 9) link_ALPHA1-3 : angle 2.81614 ( 27) link_ALPHA1-6 : bond 0.00506 ( 9) link_ALPHA1-6 : angle 2.29952 ( 27) link_BETA1-4 : bond 0.00278 ( 15) link_BETA1-4 : angle 1.44817 ( 45) link_NAG-ASN : bond 0.00528 ( 18) link_NAG-ASN : angle 2.38904 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.857 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 27 LYS cc_start: 0.8598 (pptt) cc_final: 0.7974 (mptt) REVERT: B 76 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.8281 (tpt-90) REVERT: B 103 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8720 (mm-30) REVERT: B 118 LEU cc_start: 0.9462 (tt) cc_final: 0.9163 (pp) REVERT: C 27 LYS cc_start: 0.7395 (mptt) cc_final: 0.7131 (mptt) REVERT: C 168 MET cc_start: 0.8733 (tpp) cc_final: 0.8474 (tpp) REVERT: C 268 MET cc_start: 0.8603 (ttm) cc_final: 0.8226 (ttt) REVERT: E 18 HIS cc_start: 0.8242 (p-80) cc_final: 0.7697 (p-80) REVERT: E 27 LYS cc_start: 0.8738 (ptmm) cc_final: 0.8512 (ptmm) REVERT: G 87 ASP cc_start: 0.8271 (t0) cc_final: 0.8058 (t0) REVERT: G 143 ASN cc_start: 0.8286 (m-40) cc_final: 0.7454 (p0) REVERT: G 148 GLU cc_start: 0.8331 (pm20) cc_final: 0.8071 (pm20) REVERT: G 191 TYR cc_start: 0.8711 (t80) cc_final: 0.8377 (t80) REVERT: G 197 TYR cc_start: 0.8474 (m-10) cc_final: 0.7986 (m-80) REVERT: H 121 MET cc_start: 0.9078 (tpt) cc_final: 0.8469 (tpt) REVERT: I 191 TYR cc_start: 0.7945 (t80) cc_final: 0.7489 (t80) REVERT: J 10 GLU cc_start: 0.8548 (tp30) cc_final: 0.7950 (tm-30) REVERT: J 81 MET cc_start: 0.8340 (tmm) cc_final: 0.8132 (tmm) REVERT: J 106 MET cc_start: 0.8982 (mtm) cc_final: 0.8719 (mtm) REVERT: J 121 MET cc_start: 0.9194 (tpt) cc_final: 0.8842 (tpt) REVERT: J 164 TRP cc_start: 0.6702 (m100) cc_final: 0.6039 (m100) REVERT: K 174 LYS cc_start: 0.8187 (pttt) cc_final: 0.7786 (tptp) REVERT: L 121 MET cc_start: 0.9183 (tpt) cc_final: 0.8589 (tpt) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.1571 time to fit residues: 53.1370 Evaluate side-chains 160 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 7.9990 chunk 141 optimal weight: 0.0870 chunk 158 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN F 42 GLN G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035854 restraints weight = 184549.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.036817 restraints weight = 109799.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037442 restraints weight = 77106.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037868 restraints weight = 60659.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038164 restraints weight = 51450.421| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21954 Z= 0.188 Angle : 0.669 12.059 29922 Z= 0.330 Chirality : 0.047 0.302 3486 Planarity : 0.005 0.070 3753 Dihedral : 7.623 57.118 3960 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.52 (0.16), residues: 2649 helix: 1.23 (0.25), residues: 402 sheet: 0.15 (0.18), residues: 804 loop : -1.11 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 123 TYR 0.034 0.002 TYR F 83 PHE 0.024 0.002 PHE C 294 TRP 0.034 0.002 TRP C 222 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00403 (21870) covalent geometry : angle 0.64794 (29700) SS BOND : bond 0.00356 ( 30) SS BOND : angle 1.14530 ( 60) hydrogen bonds : bond 0.03401 ( 879) hydrogen bonds : angle 5.45569 ( 2346) link_ALPHA1-2 : bond 0.00875 ( 3) link_ALPHA1-2 : angle 1.16714 ( 9) link_ALPHA1-3 : bond 0.00469 ( 9) link_ALPHA1-3 : angle 2.75798 ( 27) link_ALPHA1-6 : bond 0.00433 ( 9) link_ALPHA1-6 : angle 2.65610 ( 27) link_BETA1-4 : bond 0.00251 ( 15) link_BETA1-4 : angle 1.50558 ( 45) link_NAG-ASN : bond 0.00562 ( 18) link_NAG-ASN : angle 2.45517 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.620 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 27 LYS cc_start: 0.8714 (pptt) cc_final: 0.7956 (mptt) REVERT: B 76 ARG cc_start: 0.8498 (ttt-90) cc_final: 0.8184 (tpt-90) REVERT: B 103 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8894 (tp30) REVERT: C 27 LYS cc_start: 0.7280 (mptt) cc_final: 0.7028 (mptt) REVERT: C 168 MET cc_start: 0.8789 (tpp) cc_final: 0.8513 (tpp) REVERT: C 268 MET cc_start: 0.8638 (ttm) cc_final: 0.8394 (ttt) REVERT: E 18 HIS cc_start: 0.8215 (p-80) cc_final: 0.7701 (p-80) REVERT: E 27 LYS cc_start: 0.8712 (ptmm) cc_final: 0.8419 (ptmm) REVERT: F 91 LEU cc_start: 0.9495 (mm) cc_final: 0.9289 (mm) REVERT: G 143 ASN cc_start: 0.8392 (m-40) cc_final: 0.7495 (p0) REVERT: G 148 GLU cc_start: 0.8451 (pm20) cc_final: 0.8224 (pm20) REVERT: G 197 TYR cc_start: 0.8375 (m-10) cc_final: 0.7427 (m-80) REVERT: I 191 TYR cc_start: 0.8009 (t80) cc_final: 0.7550 (t80) REVERT: J 10 GLU cc_start: 0.8611 (tp30) cc_final: 0.7949 (tm-30) REVERT: J 81 MET cc_start: 0.8577 (tmm) cc_final: 0.8318 (tmm) REVERT: J 121 MET cc_start: 0.9217 (tpt) cc_final: 0.8854 (tpt) REVERT: J 164 TRP cc_start: 0.6707 (m100) cc_final: 0.6109 (m100) REVERT: K 174 LYS cc_start: 0.8213 (pttt) cc_final: 0.7828 (tptp) REVERT: L 121 MET cc_start: 0.9198 (tpt) cc_final: 0.8598 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1396 time to fit residues: 42.4878 Evaluate side-chains 149 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 60.6247 > 50: distance: 13 - 21: 9.531 distance: 21 - 22: 8.341 distance: 22 - 23: 9.463 distance: 22 - 25: 8.767 distance: 23 - 24: 29.753 distance: 23 - 29: 31.874 distance: 25 - 26: 13.461 distance: 25 - 27: 21.737 distance: 26 - 28: 22.084 distance: 29 - 30: 21.171 distance: 29 - 161: 29.831 distance: 30 - 31: 15.999 distance: 30 - 33: 11.894 distance: 31 - 32: 21.891 distance: 31 - 37: 23.565 distance: 32 - 176: 17.449 distance: 33 - 34: 40.549 distance: 34 - 35: 21.062 distance: 34 - 36: 27.384 distance: 37 - 38: 17.782 distance: 38 - 39: 7.042 distance: 38 - 41: 7.278 distance: 39 - 40: 8.096 distance: 39 - 45: 15.598 distance: 41 - 42: 12.235 distance: 42 - 43: 4.606 distance: 42 - 44: 6.509 distance: 45 - 46: 10.392 distance: 45 - 179: 7.704 distance: 46 - 47: 14.724 distance: 47 - 48: 14.075 distance: 49 - 50: 14.344 distance: 50 - 51: 10.106 distance: 50 - 53: 4.965 distance: 51 - 52: 14.412 distance: 51 - 57: 9.947 distance: 53 - 54: 8.710 distance: 53 - 55: 30.895 distance: 54 - 56: 11.510 distance: 57 - 58: 12.968 distance: 58 - 59: 5.699 distance: 58 - 61: 12.015 distance: 59 - 60: 15.390 distance: 59 - 65: 21.432 distance: 61 - 62: 10.851 distance: 62 - 63: 12.861 distance: 62 - 64: 12.017 distance: 65 - 66: 7.964 distance: 66 - 67: 10.582 distance: 66 - 69: 11.249 distance: 67 - 68: 11.154 distance: 67 - 71: 3.734 distance: 69 - 70: 10.157 distance: 70 - 133: 24.151 distance: 71 - 72: 5.413 distance: 72 - 73: 8.469 distance: 72 - 75: 4.365 distance: 73 - 74: 9.249 distance: 73 - 78: 4.346 distance: 74 - 102: 13.841 distance: 75 - 76: 5.104 distance: 75 - 77: 7.374 distance: 78 - 79: 4.255 distance: 79 - 80: 5.170 distance: 79 - 82: 6.922 distance: 80 - 81: 13.352 distance: 80 - 86: 9.458 distance: 81 - 107: 6.726 distance: 82 - 83: 3.182 distance: 83 - 84: 9.210 distance: 83 - 85: 10.865 distance: 86 - 87: 13.186 distance: 87 - 88: 17.996 distance: 87 - 90: 20.377 distance: 88 - 89: 11.211 distance: 88 - 94: 5.697 distance: 89 - 114: 10.811 distance: 90 - 91: 11.972 distance: 90 - 92: 7.732 distance: 91 - 93: 4.011