Starting phenix.real_space_refine on Sat Jul 4 14:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_22654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_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_22654/07_2026/7k3a_22654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_22654.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_22654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_22654.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_22654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k3a_22654/07_2026/7k3a_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.24 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.83 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: 4.11 Time building geometry restraints manager: 2.51 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 - 17.36: 11555 17.36 - 34.73: 955 34.73 - 52.09: 142 52.09 - 69.46: 33 69.46 - 86.82: 11 Dihedral angle restraints: 12696 sinusoidal: 4989 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 12693 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.100 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 12.802 86.821 7674 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 are 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/Z covalent geometry : bond 0.00430 / 0.21 (21870) covalent geometry : angle 0.81782 / 0.42 (29700) SS BOND : bond 0.06712 / 4.01 ( 30) SS BOND : angle 2.86381 / 1.77 ( 60) hydrogen bonds : bond 0.15341 / 9.66 ( 879) hydrogen bonds : angle 7.11670 / 5.02 ( 2346) link_ALPHA1-2 : bond 0.01334 / 0.67 ( 3) link_ALPHA1-2 : angle 2.44007 / 1.15 ( 9) link_ALPHA1-3 : bond 0.00849 / 0.50 ( 9) link_ALPHA1-3 : angle 4.32139 / 2.51 ( 27) link_ALPHA1-6 : bond 0.00952 / 0.63 ( 9) link_ALPHA1-6 : angle 4.11344 / 2.38 ( 27) link_BETA1-4 : bond 0.00497 / 0.35 ( 15) link_BETA1-4 : angle 2.09966 / 1.29 ( 45) link_NAG-ASN : bond 0.00423 / 0.27 ( 18) link_NAG-ASN : angle 3.24360 / 2.06 ( 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 : 0.828 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: 0.1963 time to fit residues: 139.9441 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 : 0.836 ------------------------------------------------------------------------------- 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... ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.048928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037778 restraints weight = 178724.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038792 restraints weight = 106402.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039460 restraints weight = 74784.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039905 restraints weight = 59111.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040189 restraints weight = 50423.940| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 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 = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21954 Z= 0.206 Angle : 0.719 9.605 29922 Z= 0.361 Chirality : 0.048 0.323 3486 Planarity : 0.006 0.109 3753 Dihedral : 5.014 20.170 2880 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.48 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2649 helix: 2.06 (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 0.008 0.001 ARG B 127 TYR 0.020 0.002 TYR C 233 PHE 0.030 0.002 PHE F 171 TRP 0.017 0.002 TRP K 153 HIS 0.012 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (21870) covalent geometry : angle 0.69915 / 0.36 (29700) SS BOND : bond 0.00352 / 0.24 ( 30) SS BOND : angle 0.95200 / 0.58 ( 60) hydrogen bonds : bond 0.03894 / 2.56 ( 879) hydrogen bonds : angle 5.94810 / 4.20 ( 2346) link_ALPHA1-2 : bond 0.00781 / 0.39 ( 3) link_ALPHA1-2 : angle 1.48616 / 0.80 ( 9) link_ALPHA1-3 : bond 0.00721 / 0.41 ( 9) link_ALPHA1-3 : angle 2.66099 / 1.56 ( 27) link_ALPHA1-6 : bond 0.00948 / 0.62 ( 9) link_ALPHA1-6 : angle 2.76923 / 1.68 ( 27) link_BETA1-4 : bond 0.00280 / 0.17 ( 15) link_BETA1-4 : angle 1.70153 / 1.02 ( 45) link_NAG-ASN : bond 0.00518 / 0.31 ( 18) link_NAG-ASN : angle 2.52397 / 1.61 ( 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 284 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 0.707 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: 0.8777 (p0) cc_final: 0.8529 (m-30) REVERT: A 82 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8588 (mm-30) REVERT: B 9 PHE cc_start: 0.8442 (p90) cc_final: 0.8161 (p90) REVERT: B 73 VAL cc_start: 0.9447 (t) cc_final: 0.8677 (t) REVERT: B 76 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: D 78 GLN cc_start: 0.8255 (tt0) cc_final: 0.7943 (tm-30) REVERT: D 83 TYR cc_start: 0.8901 (t80) cc_final: 0.8630 (t80) REVERT: D 95 ASN cc_start: 0.9181 (m-40) cc_final: 0.8925 (m-40) REVERT: E 18 HIS cc_start: 0.8483 (p-80) cc_final: 0.7313 (p-80) REVERT: E 27 LYS cc_start: 0.8559 (ptmm) cc_final: 0.8077 (mptt) REVERT: E 190 GLU cc_start: 0.9117 (tt0) cc_final: 0.8854 (tt0) REVERT: F 9 PHE cc_start: 0.8402 (p90) cc_final: 0.8086 (p90) REVERT: F 21 TRP cc_start: 0.9322 (m100) cc_final: 0.8898 (m100) REVERT: F 133 MET cc_start: 0.6625 (mtm) cc_final: 0.6402 (mmp) REVERT: F 163 ARG cc_start: 0.7231 (ttt90) cc_final: 0.6977 (mtm180) REVERT: G 143 ASN cc_start: 0.8821 (m-40) cc_final: 0.7895 (p0) REVERT: G 159 LEU cc_start: 0.8043 (tp) cc_final: 0.7822 (tt) REVERT: G 197 TYR cc_start: 0.8343 (m-10) cc_final: 0.7918 (m-80) REVERT: I 191 TYR cc_start: 0.8093 (t80) cc_final: 0.7617 (t80) REVERT: I 193 LYS cc_start: 0.9535 (ptmt) cc_final: 0.9305 (ptmm) REVERT: J 98 ARG cc_start: 0.8711 (ttp-170) cc_final: 0.8088 (ttp-170) REVERT: J 106 MET cc_start: 0.8826 (mtm) cc_final: 0.8606 (mtm) REVERT: J 121 MET cc_start: 0.9227 (tpt) cc_final: 0.8750 (tpt) REVERT: J 164 TRP cc_start: 0.6591 (m100) cc_final: 0.6013 (m100) REVERT: K 174 LYS cc_start: 0.8272 (pttt) cc_final: 0.7817 (tptp) REVERT: L 81 MET cc_start: 0.8668 (ttp) cc_final: 0.8028 (tmm) REVERT: L 121 MET cc_start: 0.9230 (tpt) cc_final: 0.8714 (tpt) REVERT: L 148 LEU cc_start: 0.7785 (mt) cc_final: 0.7396 (pt) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.1740 time to fit residues: 72.3301 Evaluate side-chains 185 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 2.9990 chunk 228 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 159 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035793 restraints weight = 189899.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036725 restraints weight = 114655.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037367 restraints weight = 81479.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037761 restraints weight = 64367.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.038049 restraints weight = 55257.701| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21954 Z= 0.304 Angle : 0.788 9.621 29922 Z= 0.394 Chirality : 0.048 0.285 3486 Planarity : 0.006 0.049 3753 Dihedral : 5.205 20.538 2880 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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 are not related in a simple way. whole: -0.75 (0.16), residues: 2649 helix: 1.09 (0.24), residues: 402 sheet: 0.01 (0.17), residues: 819 loop : -1.30 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 17 TYR 0.019 0.002 TYR H 111 PHE 0.021 0.002 PHE L 176 TRP 0.019 0.002 TRP E 84 HIS 0.010 0.002 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.30 (21870) covalent geometry : angle 0.76977 / 0.39 (29700) SS BOND : bond 0.00490 / 0.35 ( 30) SS BOND : angle 1.16725 / 0.68 ( 60) hydrogen bonds : bond 0.04074 / 2.69 ( 879) hydrogen bonds : angle 5.99638 / 4.24 ( 2346) link_ALPHA1-2 : bond 0.00828 / 0.42 ( 3) link_ALPHA1-2 : angle 1.16972 / 0.63 ( 9) link_ALPHA1-3 : bond 0.00448 / 0.27 ( 9) link_ALPHA1-3 : angle 2.63883 / 1.55 ( 27) link_ALPHA1-6 : bond 0.00717 / 0.42 ( 9) link_ALPHA1-6 : angle 2.71042 / 1.70 ( 27) link_BETA1-4 : bond 0.00366 / 0.23 ( 15) link_BETA1-4 : angle 1.56813 / 0.95 ( 45) link_NAG-ASN : bond 0.00638 / 0.39 ( 18) link_NAG-ASN : angle 2.63043 / 1.68 ( 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 227 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.778 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: B 9 PHE cc_start: 0.8522 (p90) cc_final: 0.8287 (p90) REVERT: C 168 MET cc_start: 0.8385 (tpp) cc_final: 0.7906 (ttp) REVERT: C 268 MET cc_start: 0.8572 (ttm) cc_final: 0.8363 (ttm) REVERT: D 17 MET cc_start: 0.2194 (mtm) cc_final: 0.1899 (mtp) REVERT: D 83 TYR cc_start: 0.8859 (t80) cc_final: 0.8651 (t80) REVERT: E 27 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8083 (mptt) REVERT: E 32 ASP cc_start: 0.8833 (m-30) cc_final: 0.8423 (p0) REVERT: E 190 GLU cc_start: 0.9203 (tt0) cc_final: 0.8951 (tt0) REVERT: G 148 GLU cc_start: 0.8339 (pm20) cc_final: 0.7984 (pm20) REVERT: G 197 TYR cc_start: 0.8444 (m-10) cc_final: 0.8031 (m-80) REVERT: H 81 MET cc_start: 0.8477 (tmm) cc_final: 0.8242 (tmm) REVERT: I 36 HIS cc_start: 0.7304 (m170) cc_final: 0.6975 (m170) REVERT: I 143 ASN cc_start: 0.8546 (m-40) cc_final: 0.7337 (p0) REVERT: I 191 TYR cc_start: 0.8144 (t80) cc_final: 0.7767 (t80) REVERT: J 81 MET cc_start: 0.8507 (tmm) cc_final: 0.8225 (tmm) REVERT: J 106 MET cc_start: 0.8887 (mtm) cc_final: 0.8648 (mtm) REVERT: J 121 MET cc_start: 0.9262 (tpt) cc_final: 0.8913 (tpt) REVERT: K 143 ASN cc_start: 0.8650 (m-40) cc_final: 0.7555 (p0) REVERT: K 174 LYS cc_start: 0.8223 (pttt) cc_final: 0.7789 (tptp) REVERT: L 10 GLU cc_start: 0.8710 (tp30) cc_final: 0.8318 (tm-30) REVERT: L 81 MET cc_start: 0.8568 (ttp) cc_final: 0.7986 (tmm) REVERT: L 106 MET cc_start: 0.8791 (mtm) cc_final: 0.8486 (mtm) REVERT: L 121 MET cc_start: 0.9239 (tpt) cc_final: 0.8700 (tpt) REVERT: L 148 LEU cc_start: 0.7869 (mt) cc_final: 0.7358 (pt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1821 time to fit residues: 60.3876 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 : 0.796 ------------------------------------------------------------------------------- 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: 0.9980 chunk 215 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 202 optimal weight: 0.0060 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3329 r_free = 0.3329 target = 0.047871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037144 restraints weight = 181530.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038156 restraints weight = 107410.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038846 restraints weight = 75326.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039292 restraints weight = 58776.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039605 restraints weight = 49691.619| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 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 = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21954 Z= 0.127 Angle : 0.650 9.646 29922 Z= 0.322 Chirality : 0.047 0.296 3486 Planarity : 0.005 0.078 3753 Dihedral : 4.849 23.724 2880 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % 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 are not related in a simple way. whole: -0.54 (0.16), residues: 2649 helix: 1.34 (0.25), residues: 402 sheet: 0.09 (0.17), residues: 825 loop : -1.14 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 123 TYR 0.026 0.002 TYR K 191 PHE 0.027 0.001 PHE L 176 TRP 0.013 0.001 TRP L 47 HIS 0.007 0.001 HIS F 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (21870) covalent geometry : angle 0.63323 / 0.32 (29700) SS BOND : bond 0.00300 / 0.21 ( 30) SS BOND : angle 0.78715 / 0.47 ( 60) hydrogen bonds : bond 0.03481 / 2.27 ( 879) hydrogen bonds : angle 5.59393 / 3.95 ( 2346) link_ALPHA1-2 : bond 0.00971 / 0.49 ( 3) link_ALPHA1-2 : angle 1.47159 / 0.79 ( 9) link_ALPHA1-3 : bond 0.00110 / 0.06 ( 9) link_ALPHA1-3 : angle 2.55606 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00330 / 0.20 ( 9) link_ALPHA1-6 : angle 1.95491 / 1.23 ( 27) link_BETA1-4 : bond 0.00261 / 0.18 ( 15) link_BETA1-4 : angle 1.33660 / 0.81 ( 45) link_NAG-ASN : bond 0.00515 / 0.30 ( 18) link_NAG-ASN : angle 2.36867 / 1.54 ( 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 244 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.830 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 320 MET cc_start: 0.7917 (ptp) cc_final: 0.7525 (ptt) REVERT: B 9 PHE cc_start: 0.8578 (p90) cc_final: 0.8257 (p90) REVERT: B 100 VAL cc_start: 0.9724 (t) cc_final: 0.9417 (t) REVERT: C 268 MET cc_start: 0.8534 (ttm) cc_final: 0.8285 (ttt) REVERT: D 17 MET cc_start: 0.1700 (mtm) cc_final: 0.1356 (mtp) REVERT: D 83 TYR cc_start: 0.8869 (t80) cc_final: 0.8635 (t80) REVERT: E 18 HIS cc_start: 0.8270 (p-80) cc_final: 0.7867 (p-80) REVERT: E 27 LYS cc_start: 0.8673 (ptmm) cc_final: 0.8265 (mptt) REVERT: E 190 GLU cc_start: 0.9214 (tt0) cc_final: 0.8961 (tt0) REVERT: G 197 TYR cc_start: 0.8356 (m-10) cc_final: 0.7842 (m-80) REVERT: H 81 MET cc_start: 0.8450 (tmm) cc_final: 0.8238 (tmm) REVERT: H 121 MET cc_start: 0.9014 (tpt) cc_final: 0.8305 (tpt) REVERT: H 164 TRP cc_start: 0.6696 (m100) cc_final: 0.6411 (m100) REVERT: I 191 TYR cc_start: 0.7943 (t80) cc_final: 0.7434 (t80) REVERT: J 10 GLU cc_start: 0.8789 (tp30) cc_final: 0.7948 (tm-30) REVERT: J 98 ARG cc_start: 0.8698 (ttp-170) cc_final: 0.8079 (ttp-170) REVERT: J 106 MET cc_start: 0.8883 (mtm) cc_final: 0.8573 (mtm) REVERT: J 121 MET cc_start: 0.9254 (tpt) cc_final: 0.8911 (tpt) REVERT: J 164 TRP cc_start: 0.6334 (m100) cc_final: 0.5804 (m100) REVERT: K 143 ASN cc_start: 0.8490 (m-40) cc_final: 0.7483 (p0) REVERT: K 174 LYS cc_start: 0.8228 (pttt) cc_final: 0.7775 (tptp) REVERT: L 10 GLU cc_start: 0.8674 (tp30) cc_final: 0.8375 (tm-30) REVERT: L 121 MET cc_start: 0.9227 (tpt) cc_final: 0.8655 (tpt) outliers start: 3 outliers final: 0 residues processed: 244 average time/residue: 0.1703 time to fit residues: 62.1590 Evaluate side-chains 164 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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: 0.8980 chunk 176 optimal weight: 8.9990 chunk 58 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 231 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037496 restraints weight = 180800.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.038521 restraints weight = 106878.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039215 restraints weight = 74855.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039688 restraints weight = 58435.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039970 restraints weight = 49141.212| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21954 Z= 0.115 Angle : 0.629 9.637 29922 Z= 0.311 Chirality : 0.047 0.380 3486 Planarity : 0.005 0.097 3753 Dihedral : 4.656 21.629 2880 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 are not related in a simple way. whole: -0.39 (0.16), residues: 2649 helix: 1.52 (0.24), residues: 402 sheet: 0.08 (0.17), residues: 870 loop : -1.01 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 38 TYR 0.022 0.002 TYR K 191 PHE 0.025 0.001 PHE L 176 TRP 0.011 0.001 TRP L 47 HIS 0.007 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21870) covalent geometry : angle 0.61327 / 0.31 (29700) SS BOND : bond 0.00350 / 0.24 ( 30) SS BOND : angle 0.80778 / 0.49 ( 60) hydrogen bonds : bond 0.03256 / 2.13 ( 879) hydrogen bonds : angle 5.38717 / 3.82 ( 2346) link_ALPHA1-2 : bond 0.00666 / 0.33 ( 3) link_ALPHA1-2 : angle 1.21208 / 0.67 ( 9) link_ALPHA1-3 : bond 0.00116 / 0.07 ( 9) link_ALPHA1-3 : angle 2.44194 / 1.34 ( 27) link_ALPHA1-6 : bond 0.00334 / 0.20 ( 9) link_ALPHA1-6 : angle 1.79024 / 1.12 ( 27) link_BETA1-4 : bond 0.00266 / 0.18 ( 15) link_BETA1-4 : angle 1.32042 / 0.80 ( 45) link_NAG-ASN : bond 0.00643 / 0.37 ( 18) link_NAG-ASN : angle 2.28337 / 1.51 ( 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 240 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.860 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 9 PHE cc_start: 0.8568 (p90) cc_final: 0.8266 (p90) REVERT: B 42 GLN cc_start: 0.9119 (pm20) cc_final: 0.8899 (pm20) REVERT: B 62 LYS cc_start: 0.8845 (mttp) cc_final: 0.8463 (mmmt) REVERT: B 100 VAL cc_start: 0.9701 (t) cc_final: 0.9439 (t) REVERT: C 268 MET cc_start: 0.8558 (ttm) cc_final: 0.8328 (ttt) REVERT: D 17 MET cc_start: 0.1466 (mtm) cc_final: 0.1248 (mtp) REVERT: D 83 TYR cc_start: 0.8817 (t80) cc_final: 0.8608 (t80) REVERT: E 18 HIS cc_start: 0.8216 (p-80) cc_final: 0.7809 (p-80) REVERT: E 27 LYS cc_start: 0.8688 (ptmm) cc_final: 0.8224 (mptt) REVERT: E 190 GLU cc_start: 0.9215 (tt0) cc_final: 0.8965 (tt0) REVERT: F 160 ASP cc_start: 0.8655 (m-30) cc_final: 0.8284 (p0) REVERT: G 143 ASN cc_start: 0.8517 (m-40) cc_final: 0.7688 (p0) REVERT: G 197 TYR cc_start: 0.8346 (m-10) cc_final: 0.7883 (m-80) REVERT: H 106 MET cc_start: 0.8778 (mtm) cc_final: 0.8495 (mtm) REVERT: H 121 MET cc_start: 0.9053 (tpt) cc_final: 0.8401 (tpt) REVERT: H 164 TRP cc_start: 0.6669 (m100) cc_final: 0.6440 (m100) REVERT: I 191 TYR cc_start: 0.8044 (t80) cc_final: 0.7596 (t80) REVERT: J 10 GLU cc_start: 0.8692 (tp30) cc_final: 0.8201 (tm-30) REVERT: J 81 MET cc_start: 0.8425 (tmm) cc_final: 0.8164 (tmm) REVERT: J 98 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.7875 (ttp-170) REVERT: J 106 MET cc_start: 0.8904 (mtm) cc_final: 0.8460 (mtm) REVERT: J 121 MET cc_start: 0.9219 (tpt) cc_final: 0.8853 (tpt) REVERT: J 164 TRP cc_start: 0.6504 (m100) cc_final: 0.5958 (m100) REVERT: K 174 LYS cc_start: 0.8238 (pttt) cc_final: 0.7766 (tptp) REVERT: L 121 MET cc_start: 0.9207 (tpt) cc_final: 0.8671 (tpt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1674 time to fit residues: 60.3396 Evaluate side-chains 167 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 10.0000 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 228 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 159 HIS G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 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 = 0.3290 r_free = 0.3290 target = 0.046701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036145 restraints weight = 187968.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.037129 restraints weight = 110389.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037780 restraints weight = 77540.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038242 restraints weight = 60836.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038512 restraints weight = 51261.246| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21954 Z= 0.206 Angle : 0.673 10.075 29922 Z= 0.333 Chirality : 0.046 0.314 3486 Planarity : 0.005 0.079 3753 Dihedral : 4.761 23.047 2880 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 are not related in a simple way. whole: -0.50 (0.16), residues: 2649 helix: 1.40 (0.25), residues: 402 sheet: 0.07 (0.18), residues: 807 loop : -1.09 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 17 TYR 0.022 0.002 TYR K 191 PHE 0.024 0.002 PHE L 176 TRP 0.012 0.002 TRP J 36 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (21870) covalent geometry : angle 0.65666 / 0.33 (29700) SS BOND : bond 0.00400 / 0.28 ( 30) SS BOND : angle 0.89522 / 0.53 ( 60) hydrogen bonds : bond 0.03402 / 2.24 ( 879) hydrogen bonds : angle 5.53933 / 3.93 ( 2346) link_ALPHA1-2 : bond 0.00852 / 0.42 ( 3) link_ALPHA1-2 : angle 1.15037 / 0.63 ( 9) link_ALPHA1-3 : bond 0.00226 / 0.13 ( 9) link_ALPHA1-3 : angle 2.44404 / 1.40 ( 27) link_ALPHA1-6 : bond 0.00319 / 0.18 ( 9) link_ALPHA1-6 : angle 2.24986 / 1.42 ( 27) link_BETA1-4 : bond 0.00252 / 0.16 ( 15) link_BETA1-4 : angle 1.37770 / 0.83 ( 45) link_NAG-ASN : bond 0.00570 / 0.35 ( 18) link_NAG-ASN : angle 2.38537 / 1.55 ( 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 208 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.718 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 233 TYR cc_start: 0.8405 (m-10) cc_final: 0.8146 (m-10) REVERT: B 9 PHE cc_start: 0.8610 (p90) cc_final: 0.8276 (p90) REVERT: B 62 LYS cc_start: 0.8834 (mttp) cc_final: 0.8342 (mppt) REVERT: B 100 VAL cc_start: 0.9719 (t) cc_final: 0.9412 (t) REVERT: C 268 MET cc_start: 0.8593 (ttm) cc_final: 0.8374 (ttt) REVERT: D 17 MET cc_start: 0.2197 (mtm) cc_final: 0.1974 (mtm) REVERT: D 83 TYR cc_start: 0.8876 (t80) cc_final: 0.8648 (t80) REVERT: E 18 HIS cc_start: 0.8264 (p-80) cc_final: 0.7836 (p-80) REVERT: E 27 LYS cc_start: 0.8689 (ptmm) cc_final: 0.8223 (mptt) REVERT: E 190 GLU cc_start: 0.9241 (tt0) cc_final: 0.8966 (tt0) REVERT: G 197 TYR cc_start: 0.8395 (m-10) cc_final: 0.7956 (m-80) REVERT: H 106 MET cc_start: 0.8753 (mtm) cc_final: 0.8494 (mtm) REVERT: H 121 MET cc_start: 0.9098 (tpt) cc_final: 0.8455 (tpt) REVERT: I 36 HIS cc_start: 0.7158 (m170) cc_final: 0.6894 (m170) REVERT: I 191 TYR cc_start: 0.8045 (t80) cc_final: 0.7507 (t80) REVERT: J 10 GLU cc_start: 0.8700 (tp30) cc_final: 0.8009 (tm-30) REVERT: J 81 MET cc_start: 0.8463 (tmm) cc_final: 0.8203 (tmm) REVERT: J 106 MET cc_start: 0.8962 (mtm) cc_final: 0.8652 (mtm) REVERT: J 121 MET cc_start: 0.9243 (tpt) cc_final: 0.8875 (tpt) REVERT: J 164 TRP cc_start: 0.6605 (m100) cc_final: 0.6050 (m100) REVERT: K 174 LYS cc_start: 0.8180 (pttt) cc_final: 0.7756 (tptp) REVERT: L 121 MET cc_start: 0.9218 (tpt) cc_final: 0.8609 (tpt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1585 time to fit residues: 50.2351 Evaluate side-chains 155 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 0.5980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 30.0000 chunk 131 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 40 GLN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 GLN ** 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** L 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.047626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.037089 restraints weight = 181380.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.038084 restraints weight = 107504.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038762 restraints weight = 75198.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039226 restraints weight = 58786.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039517 restraints weight = 49392.976| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21954 Z= 0.121 Angle : 0.630 10.259 29922 Z= 0.309 Chirality : 0.047 0.311 3486 Planarity : 0.005 0.052 3753 Dihedral : 4.590 22.605 2880 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.09 % Allowed : 1.03 % Favored : 98.88 % 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 are not related in a simple way. whole: -0.38 (0.16), residues: 2649 helix: 1.49 (0.25), residues: 402 sheet: 0.15 (0.18), residues: 825 loop : -1.02 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 123 TYR 0.019 0.001 TYR F 83 PHE 0.025 0.001 PHE L 176 TRP 0.016 0.001 TRP J 47 HIS 0.007 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21870) covalent geometry : angle 0.61473 / 0.31 (29700) SS BOND : bond 0.00294 / 0.21 ( 30) SS BOND : angle 0.71682 / 0.44 ( 60) hydrogen bonds : bond 0.03241 / 2.11 ( 879) hydrogen bonds : angle 5.34748 / 3.80 ( 2346) link_ALPHA1-2 : bond 0.00694 / 0.35 ( 3) link_ALPHA1-2 : angle 1.19359 / 0.66 ( 9) link_ALPHA1-3 : bond 0.00178 / 0.09 ( 9) link_ALPHA1-3 : angle 2.46931 / 1.36 ( 27) link_ALPHA1-6 : bond 0.00356 / 0.22 ( 9) link_ALPHA1-6 : angle 1.83049 / 1.15 ( 27) link_BETA1-4 : bond 0.00248 / 0.17 ( 15) link_BETA1-4 : angle 1.23637 / 0.75 ( 45) link_NAG-ASN : bond 0.00523 / 0.30 ( 18) link_NAG-ASN : angle 2.30195 / 1.51 ( 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 228 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.916 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: B 9 PHE cc_start: 0.8589 (p90) cc_final: 0.8249 (p90) REVERT: B 62 LYS cc_start: 0.8819 (mttp) cc_final: 0.8272 (mppt) REVERT: B 100 VAL cc_start: 0.9703 (t) cc_final: 0.9450 (t) REVERT: B 103 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8772 (mm-30) REVERT: B 118 LEU cc_start: 0.9453 (tt) cc_final: 0.9196 (pp) REVERT: C 233 TYR cc_start: 0.8398 (m-10) cc_final: 0.8176 (m-10) REVERT: C 268 MET cc_start: 0.8626 (ttm) cc_final: 0.8364 (ttt) REVERT: D 83 TYR cc_start: 0.8849 (t80) cc_final: 0.8621 (t80) REVERT: E 18 HIS cc_start: 0.8192 (p-80) cc_final: 0.7682 (p-80) REVERT: E 27 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8211 (mptt) REVERT: E 190 GLU cc_start: 0.9237 (tt0) cc_final: 0.8924 (tt0) REVERT: E 233 TYR cc_start: 0.8416 (m-10) cc_final: 0.8203 (m-10) REVERT: F 42 GLN cc_start: 0.9144 (pm20) cc_final: 0.8842 (pm20) REVERT: F 83 TYR cc_start: 0.9053 (t80) cc_final: 0.8487 (t80) REVERT: F 118 LEU cc_start: 0.9514 (tt) cc_final: 0.9106 (pp) REVERT: F 133 MET cc_start: 0.5804 (mmp) cc_final: 0.5563 (mpp) REVERT: G 87 ASP cc_start: 0.8282 (t0) cc_final: 0.8040 (t0) REVERT: G 143 ASN cc_start: 0.8603 (m-40) cc_final: 0.7652 (p0) REVERT: G 197 TYR cc_start: 0.8409 (m-10) cc_final: 0.7931 (m-80) REVERT: H 121 MET cc_start: 0.9085 (tpt) cc_final: 0.8490 (tpt) REVERT: H 164 TRP cc_start: 0.6456 (m100) cc_final: 0.6230 (m100) REVERT: I 36 HIS cc_start: 0.7168 (m170) cc_final: 0.6930 (m170) REVERT: I 191 TYR cc_start: 0.8069 (t80) cc_final: 0.7585 (t80) REVERT: J 10 GLU cc_start: 0.8637 (tp30) cc_final: 0.8163 (tm-30) REVERT: J 81 MET cc_start: 0.8364 (tmm) cc_final: 0.8075 (tmm) REVERT: J 106 MET cc_start: 0.8892 (mtm) cc_final: 0.8637 (mtm) REVERT: J 121 MET cc_start: 0.9229 (tpt) cc_final: 0.8851 (tpt) REVERT: J 164 TRP cc_start: 0.6598 (m100) cc_final: 0.5992 (m100) REVERT: K 174 LYS cc_start: 0.8170 (pttt) cc_final: 0.7798 (tptp) REVERT: L 121 MET cc_start: 0.9197 (tpt) cc_final: 0.8594 (tpt) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.1549 time to fit residues: 54.3858 Evaluate side-chains 170 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 = 0.3323 r_free = 0.3323 target = 0.047664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037136 restraints weight = 182151.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.038141 restraints weight = 107869.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038810 restraints weight = 75648.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039232 restraints weight = 59222.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039571 restraints weight = 50264.137| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4625 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 : 0.617 10.519 29922 Z= 0.303 Chirality : 0.046 0.314 3486 Planarity : 0.004 0.053 3753 Dihedral : 4.457 22.717 2880 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 are not related in a simple way. whole: -0.32 (0.16), residues: 2649 helix: 1.64 (0.25), residues: 402 sheet: 0.28 (0.18), residues: 804 loop : -1.06 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 127 TYR 0.024 0.001 TYR B 83 PHE 0.022 0.001 PHE L 176 TRP 0.010 0.001 TRP J 47 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (21870) covalent geometry : angle 0.60151 / 0.30 (29700) SS BOND : bond 0.00299 / 0.21 ( 30) SS BOND : angle 0.80193 / 0.48 ( 60) hydrogen bonds : bond 0.03192 / 2.09 ( 879) hydrogen bonds : angle 5.24232 / 3.73 ( 2346) link_ALPHA1-2 : bond 0.00685 / 0.34 ( 3) link_ALPHA1-2 : angle 1.22086 / 0.68 ( 9) link_ALPHA1-3 : bond 0.00148 / 0.08 ( 9) link_ALPHA1-3 : angle 2.40656 / 1.33 ( 27) link_ALPHA1-6 : bond 0.00322 / 0.19 ( 9) link_ALPHA1-6 : angle 1.80938 / 1.14 ( 27) link_BETA1-4 : bond 0.00247 / 0.17 ( 15) link_BETA1-4 : angle 1.24847 / 0.76 ( 45) link_NAG-ASN : bond 0.00517 / 0.30 ( 18) link_NAG-ASN : angle 2.31501 / 1.52 ( 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 218 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.842 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: B 9 PHE cc_start: 0.8642 (p90) cc_final: 0.8239 (p90) REVERT: B 62 LYS cc_start: 0.8765 (mttp) cc_final: 0.8280 (mppt) REVERT: B 100 VAL cc_start: 0.9693 (t) cc_final: 0.9465 (t) REVERT: B 103 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8771 (mm-30) REVERT: C 27 LYS cc_start: 0.8536 (pptt) cc_final: 0.8148 (mptt) REVERT: C 233 TYR cc_start: 0.8391 (m-10) cc_final: 0.8181 (m-10) REVERT: D 17 MET cc_start: 0.1662 (mtm) cc_final: 0.1170 (mtp) REVERT: E 18 HIS cc_start: 0.8169 (p-80) cc_final: 0.7654 (p-80) REVERT: E 27 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8195 (mptt) REVERT: E 190 GLU cc_start: 0.9235 (tt0) cc_final: 0.8920 (tt0) REVERT: F 76 ARG cc_start: 0.8335 (ttt180) cc_final: 0.8103 (ttt180) REVERT: F 118 LEU cc_start: 0.9422 (tt) cc_final: 0.9119 (pp) REVERT: F 133 MET cc_start: 0.5650 (mmp) cc_final: 0.5431 (mpp) REVERT: G 197 TYR cc_start: 0.8357 (m-10) cc_final: 0.7874 (m-80) REVERT: H 121 MET cc_start: 0.9065 (tpt) cc_final: 0.8493 (tpt) REVERT: H 164 TRP cc_start: 0.6575 (m100) cc_final: 0.6367 (m100) REVERT: I 36 HIS cc_start: 0.7140 (m170) cc_final: 0.6902 (m170) REVERT: I 191 TYR cc_start: 0.8039 (t80) cc_final: 0.7557 (t80) REVERT: J 81 MET cc_start: 0.8354 (tmm) cc_final: 0.8137 (tmm) REVERT: J 106 MET cc_start: 0.8907 (mtm) cc_final: 0.8674 (mtm) REVERT: J 121 MET cc_start: 0.9212 (tpt) cc_final: 0.8829 (tpt) REVERT: J 164 TRP cc_start: 0.6589 (m100) cc_final: 0.6032 (m100) REVERT: K 174 LYS cc_start: 0.8173 (pttt) cc_final: 0.7795 (tptp) REVERT: L 54 TYR cc_start: 0.7711 (t80) cc_final: 0.7439 (t80) REVERT: L 121 MET cc_start: 0.9188 (tpt) cc_final: 0.8609 (tpt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1509 time to fit residues: 50.9162 Evaluate side-chains 162 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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: 10.0000 chunk 141 optimal weight: 0.0670 chunk 158 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 171 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.047911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037358 restraints weight = 181938.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038358 restraints weight = 107763.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.039033 restraints weight = 75480.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039459 restraints weight = 59031.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.039770 restraints weight = 49995.754| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21954 Z= 0.113 Angle : 0.618 11.041 29922 Z= 0.302 Chirality : 0.046 0.316 3486 Planarity : 0.004 0.052 3753 Dihedral : 4.356 22.593 2880 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % 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 are not related in a simple way. whole: -0.26 (0.16), residues: 2649 helix: 1.73 (0.25), residues: 402 sheet: 0.33 (0.18), residues: 804 loop : -1.04 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 127 TYR 0.021 0.001 TYR B 83 PHE 0.021 0.001 PHE L 176 TRP 0.008 0.001 TRP L 47 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21870) covalent geometry : angle 0.60199 / 0.30 (29700) SS BOND : bond 0.00294 / 0.21 ( 30) SS BOND : angle 0.97902 / 0.63 ( 60) hydrogen bonds : bond 0.03137 / 2.05 ( 879) hydrogen bonds : angle 5.15190 / 3.66 ( 2346) link_ALPHA1-2 : bond 0.00677 / 0.34 ( 3) link_ALPHA1-2 : angle 1.21725 / 0.68 ( 9) link_ALPHA1-3 : bond 0.00204 / 0.11 ( 9) link_ALPHA1-3 : angle 2.39611 / 1.32 ( 27) link_ALPHA1-6 : bond 0.00364 / 0.22 ( 9) link_ALPHA1-6 : angle 1.75347 / 1.10 ( 27) link_BETA1-4 : bond 0.00262 / 0.18 ( 15) link_BETA1-4 : angle 1.21270 / 0.74 ( 45) link_NAG-ASN : bond 0.00521 / 0.30 ( 18) link_NAG-ASN : angle 2.31096 / 1.53 ( 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 232 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.876 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: A 27 LYS cc_start: 0.8594 (pptt) cc_final: 0.7950 (mptt) REVERT: B 9 PHE cc_start: 0.8657 (p90) cc_final: 0.8351 (p90) REVERT: B 42 GLN cc_start: 0.9252 (pm20) cc_final: 0.8972 (pm20) REVERT: B 62 LYS cc_start: 0.8760 (mttp) cc_final: 0.8243 (mppt) REVERT: B 103 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8778 (mm-30) REVERT: B 118 LEU cc_start: 0.9442 (tt) cc_final: 0.9164 (pp) REVERT: C 27 LYS cc_start: 0.8355 (pptt) cc_final: 0.8089 (mptt) REVERT: C 233 TYR cc_start: 0.8493 (m-10) cc_final: 0.8287 (m-10) REVERT: E 18 HIS cc_start: 0.8147 (p-80) cc_final: 0.7634 (p-80) REVERT: E 27 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8152 (mptt) REVERT: E 190 GLU cc_start: 0.9208 (tt0) cc_final: 0.8966 (tt0) REVERT: F 118 LEU cc_start: 0.9519 (tt) cc_final: 0.9131 (pp) REVERT: G 197 TYR cc_start: 0.8352 (m-10) cc_final: 0.7892 (m-80) REVERT: I 36 HIS cc_start: 0.7096 (m170) cc_final: 0.6867 (m170) REVERT: I 191 TYR cc_start: 0.8028 (t80) cc_final: 0.7553 (t80) REVERT: J 98 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.7942 (ttp-170) REVERT: J 121 MET cc_start: 0.9195 (tpt) cc_final: 0.8809 (tpt) REVERT: J 164 TRP cc_start: 0.6536 (m100) cc_final: 0.5967 (m100) REVERT: K 174 LYS cc_start: 0.8191 (pttt) cc_final: 0.7784 (tptp) REVERT: K 195 LYS cc_start: 0.8824 (mppt) cc_final: 0.8482 (mmmt) REVERT: L 54 TYR cc_start: 0.7683 (t80) cc_final: 0.7474 (t80) REVERT: L 121 MET cc_start: 0.9176 (tpt) cc_final: 0.8585 (tpt) REVERT: L 164 TRP cc_start: 0.6695 (m100) cc_final: 0.6004 (m100) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.1503 time to fit residues: 53.1669 Evaluate side-chains 169 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 129 optimal weight: 0.0060 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** 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 39 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036757 restraints weight = 185647.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037742 restraints weight = 109425.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038410 restraints weight = 76683.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038861 restraints weight = 60234.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039165 restraints weight = 50893.680| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21954 Z= 0.152 Angle : 0.646 11.942 29922 Z= 0.319 Chirality : 0.046 0.310 3486 Planarity : 0.005 0.065 3753 Dihedral : 4.424 22.673 2880 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 are not related in a simple way. whole: -0.33 (0.16), residues: 2649 helix: 1.50 (0.25), residues: 402 sheet: 0.28 (0.18), residues: 804 loop : -1.03 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 17 TYR 0.020 0.002 TYR A 105 PHE 0.020 0.002 PHE L 176 TRP 0.065 0.002 TRP H 164 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (21870) covalent geometry : angle 0.63036 / 0.32 (29700) SS BOND : bond 0.00337 / 0.24 ( 30) SS BOND : angle 1.05451 / 0.69 ( 60) hydrogen bonds : bond 0.03342 / 2.16 ( 879) hydrogen bonds : angle 5.23451 / 3.72 ( 2346) link_ALPHA1-2 : bond 0.00738 / 0.37 ( 3) link_ALPHA1-2 : angle 1.15328 / 0.64 ( 9) link_ALPHA1-3 : bond 0.00124 / 0.07 ( 9) link_ALPHA1-3 : angle 2.37571 / 1.34 ( 27) link_ALPHA1-6 : bond 0.00228 / 0.14 ( 9) link_ALPHA1-6 : angle 1.99224 / 1.26 ( 27) link_BETA1-4 : bond 0.00197 / 0.13 ( 15) link_BETA1-4 : angle 1.23551 / 0.76 ( 45) link_NAG-ASN : bond 0.00526 / 0.31 ( 18) link_NAG-ASN : angle 2.33963 / 1.54 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 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 207 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.641 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: A 27 LYS cc_start: 0.8706 (pptt) cc_final: 0.7968 (mptt) REVERT: B 62 LYS cc_start: 0.8715 (mttp) cc_final: 0.8224 (mppt) REVERT: B 103 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 118 LEU cc_start: 0.9445 (tt) cc_final: 0.9193 (pp) REVERT: C 27 LYS cc_start: 0.8350 (pptt) cc_final: 0.8078 (mptt) REVERT: D 83 TYR cc_start: 0.8868 (t80) cc_final: 0.8529 (t80) REVERT: E 18 HIS cc_start: 0.8233 (p-80) cc_final: 0.7849 (p90) REVERT: E 27 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8489 (ptmm) REVERT: E 190 GLU cc_start: 0.9195 (tt0) cc_final: 0.8875 (tt0) REVERT: E 260 MET cc_start: 0.8690 (tpp) cc_final: 0.8367 (tpp) REVERT: F 118 LEU cc_start: 0.9500 (tt) cc_final: 0.9142 (pp) REVERT: F 133 MET cc_start: 0.5582 (mpp) cc_final: 0.5229 (mpp) REVERT: G 197 TYR cc_start: 0.8441 (m-10) cc_final: 0.8025 (m-80) REVERT: I 36 HIS cc_start: 0.7089 (m170) cc_final: 0.6885 (m170) REVERT: I 191 TYR cc_start: 0.7947 (t80) cc_final: 0.7636 (t80) REVERT: J 121 MET cc_start: 0.9188 (tpt) cc_final: 0.8800 (tpt) REVERT: J 164 TRP cc_start: 0.6647 (m100) cc_final: 0.6044 (m100) REVERT: K 174 LYS cc_start: 0.8213 (pttt) cc_final: 0.7784 (tptp) REVERT: L 54 TYR cc_start: 0.7712 (t80) cc_final: 0.7481 (t80) REVERT: L 121 MET cc_start: 0.9194 (tpt) cc_final: 0.8594 (tpt) REVERT: L 164 TRP cc_start: 0.6805 (m100) cc_final: 0.6114 (m100) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1355 time to fit residues: 43.9737 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 : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 155 optimal weight: 0.0670 chunk 224 optimal weight: 0.0270 overall best weight: 1.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 39 GLN ** 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 = 0.3319 r_free = 0.3319 target = 0.047615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036942 restraints weight = 184949.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.037939 restraints weight = 109124.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038598 restraints weight = 76701.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039051 restraints weight = 60203.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039354 restraints weight = 50854.811| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21954 Z= 0.131 Angle : 0.631 12.068 29922 Z= 0.310 Chirality : 0.046 0.311 3486 Planarity : 0.004 0.060 3753 Dihedral : 4.399 22.699 2880 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 are not related in a simple way. whole: -0.29 (0.16), residues: 2649 helix: 1.59 (0.25), residues: 399 sheet: 0.29 (0.18), residues: 804 loop : -1.00 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 127 TYR 0.018 0.001 TYR C 233 PHE 0.019 0.001 PHE L 176 TRP 0.042 0.002 TRP H 164 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (21870) covalent geometry : angle 0.61565 / 0.31 (29700) SS BOND : bond 0.00320 / 0.23 ( 30) SS BOND : angle 0.99826 / 0.64 ( 60) hydrogen bonds : bond 0.03278 / 2.12 ( 879) hydrogen bonds : angle 5.16549 / 3.66 ( 2346) link_ALPHA1-2 : bond 0.00690 / 0.35 ( 3) link_ALPHA1-2 : angle 1.12658 / 0.63 ( 9) link_ALPHA1-3 : bond 0.00172 / 0.09 ( 9) link_ALPHA1-3 : angle 2.38066 / 1.32 ( 27) link_ALPHA1-6 : bond 0.00268 / 0.16 ( 9) link_ALPHA1-6 : angle 1.83734 / 1.16 ( 27) link_BETA1-4 : bond 0.00208 / 0.14 ( 15) link_BETA1-4 : angle 1.19628 / 0.73 ( 45) link_NAG-ASN : bond 0.00517 / 0.30 ( 18) link_NAG-ASN : angle 2.31782 / 1.53 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.71 seconds wall clock time: 64 minutes 36.90 seconds (3876.90 seconds total)