Starting phenix.real_space_refine on Sun Jul 5 03:51:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hju_34838/07_2026/8hju_34838.cif" } resolution = 2.8 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= 0.008 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 7 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 17010 2.51 5 N 3312 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 23917 Number of models: 1 Model: "" Number of chains: 71 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2389 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2404 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Chain: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 404 Unusual residues: {'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'MQE': 2, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'MQE:plan-2': 1, 'MQE:plan-3': 1, 'MQE:plan-4': 1, 'MQE:plan-5': 1, 'MQE:plan-6': 1, 'MQE:plan-9': 1, 'MQE:plan-10': 1, 'MQE:plan-11': 1, 'MQE:plan-12': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 48 Chain: "N" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'KGD': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEM': 4, 'KGD': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.10, per 1000 atoms: 0.21 Number of scatterers: 23917 At special positions: 0 Unit cell: (138.24, 122.04, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 75 16.00 P 7 15.00 Mg 48 11.99 O 3460 8.00 N 3312 7.00 C 17010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=61, symmetry=0 Number of additional bonds: simple=61, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 959.0 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 3 sheets defined 68.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain '0' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 33 Processing helix chain '2' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.975A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 15 Processing helix chain 'I' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 49 through 55 Processing helix chain 'L' and resid 70 through 93 removed outlier: 4.108A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 150 Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.780A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 296 removed outlier: 4.031A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.036A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 removed outlier: 3.869A pdb=" N VAL L 314 " --> pdb=" O GLY L 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 344 Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 378 through 401 Processing helix chain 'M' and resid 404 through 412 removed outlier: 3.512A pdb=" N LEU M 409 " --> pdb=" O PRO M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 463 removed outlier: 3.576A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.558A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 561 Processing helix chain 'M' and resid 565 through 580 Processing helix chain 'M' and resid 586 through 613 removed outlier: 3.602A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 15 Processing helix chain 'U' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'V' and resid 36 through 40 Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 47 removed outlier: 3.650A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.509A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.920A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.506A pdb=" N PHE C 242 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS C 243 " --> pdb=" O CYS C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 243' Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.593A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.323A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.430A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 31 Proline residue: Y 19 - end of helix Processing helix chain 'Z' and resid 16 through 47 Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 53 through 58 Processing sheet with id=AA1, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.992A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.868A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 349 through 351 removed outlier: 3.766A pdb=" N GLY M 349 " --> pdb=" O VAL M 375 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.29: 3053 1.29 - 1.49: 11699 1.49 - 1.69: 9879 1.69 - 1.88: 126 1.88 - 2.08: 208 Bond restraints: 24965 Sorted by residual: bond pdb=" C VAL W 25 " pdb=" N HIS W 26 " ideal model delta sigma weight residual 1.335 1.432 -0.097 1.31e-02 5.83e+03 5.49e+01 bond pdb=" C1 PGV P 103 " pdb=" C2 PGV P 103 " ideal model delta sigma weight residual 1.504 1.365 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C LEU C 295 " pdb=" N CYS C 296 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.73e-02 3.34e+03 3.63e+01 bond pdb=" CAB KGD C 401 " pdb=" CAF KGD C 401 " ideal model delta sigma weight residual 1.536 1.417 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C VAL 4 25 " pdb=" N HIS 4 26 " ideal model delta sigma weight residual 1.335 1.415 -0.080 1.38e-02 5.25e+03 3.39e+01 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 31385 3.37 - 6.73: 2652 6.73 - 10.10: 538 10.10 - 13.46: 178 13.46 - 16.83: 7 Bond angle restraints: 34760 Sorted by residual: angle pdb=" N ALA V 35 " pdb=" CA ALA V 35 " pdb=" C ALA V 35 " ideal model delta sigma weight residual 111.69 99.18 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N GLY M 425 " pdb=" CA GLY M 425 " pdb=" C GLY M 425 " ideal model delta sigma weight residual 112.50 123.52 -11.02 1.16e+00 7.43e-01 9.03e+01 angle pdb=" N GLY L 307 " pdb=" CA GLY L 307 " pdb=" C GLY L 307 " ideal model delta sigma weight residual 113.37 123.41 -10.04 1.34e+00 5.57e-01 5.61e+01 angle pdb=" N PHE L 206 " pdb=" CA PHE L 206 " pdb=" C PHE L 206 " ideal model delta sigma weight residual 113.01 104.24 8.77 1.20e+00 6.94e-01 5.34e+01 angle pdb=" N THR L 97 " pdb=" CA THR L 97 " pdb=" C THR L 97 " ideal model delta sigma weight residual 111.36 119.32 -7.96 1.09e+00 8.42e-01 5.33e+01 ... (remaining 34755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 11876 28.94 - 57.87: 784 57.87 - 86.81: 103 86.81 - 115.74: 21 115.74 - 144.68: 21 Dihedral angle restraints: 12805 sinusoidal: 6082 harmonic: 6723 Sorted by residual: dihedral pdb=" C1 BCL S 102 " pdb=" CGA BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CBA BCL S 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.93 -125.07 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL F 102 " pdb=" CGA BCL F 102 " pdb=" O2A BCL F 102 " pdb=" CBA BCL F 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.97 -125.03 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL 8 101 " pdb=" CGA BCL 8 101 " pdb=" O2A BCL 8 101 " pdb=" CBA BCL 8 101 " ideal model delta sinusoidal sigma weight residual -180.00 -54.98 -125.02 1 6.00e+00 2.78e-02 4.20e+02 ... (remaining 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.118: 3408 1.118 - 2.236: 0 2.236 - 3.353: 0 3.353 - 4.471: 0 4.471 - 5.589: 16 Chirality restraints: 3424 Sorted by residual: chirality pdb=" C18 BCL X 101 " pdb=" C17 BCL X 101 " pdb=" C19 BCL X 101 " pdb=" C20 BCL X 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.88 5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C18 BCL W 102 " pdb=" C17 BCL W 102 " pdb=" C19 BCL W 102 " pdb=" C20 BCL W 102 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.71e+02 chirality pdb=" C18 BCL 5 101 " pdb=" C17 BCL 5 101 " pdb=" C19 BCL 5 101 " pdb=" C20 BCL 5 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.69e+02 ... (remaining 3421 not shown) Planarity restraints: 4222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL L1001 " 0.343 1.50e-02 4.44e+03 2.91e-01 1.88e+03 pdb=" C2 BCL L1001 " -0.400 1.50e-02 4.44e+03 pdb=" C3 BCL L1001 " -0.247 1.50e-02 4.44e+03 pdb=" C4 BCL L1001 " 0.016 1.50e-02 4.44e+03 pdb=" C5 BCL L1001 " 0.289 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL L1001 " 0.051 5.00e-03 4.00e+04 9.26e-02 1.37e+03 pdb=" CAD BCL L1001 " -0.160 5.00e-03 4.00e+04 pdb=" CBD BCL L1001 " 0.043 5.00e-03 4.00e+04 pdb=" OBD BCL L1001 " 0.066 5.00e-03 4.00e+04 delta sigma weight rms_deltas residual plane pdb=" C3D BCL B 101 " 0.043 5.00e-03 4.00e+04 7.89e-02 9.96e+02 pdb=" CAD BCL B 101 " -0.136 5.00e-03 4.00e+04 pdb=" CBD BCL B 101 " 0.036 5.00e-03 4.00e+04 pdb=" OBD BCL B 101 " 0.056 5.00e-03 4.00e+04 ... (remaining 4219 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 96 2.44 - 3.06: 14798 3.06 - 3.67: 36960 3.67 - 4.29: 62204 4.29 - 4.90: 100285 Nonbonded interactions: 214343 Sorted by model distance: nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M 702 " model vdw 1.827 2.260 nonbonded pdb=" NE2 HIS L 229 " pdb="FE FE M 702 " model vdw 2.065 2.340 nonbonded pdb=" NE2 HIS C 122 " pdb="FE HEM C 402 " model vdw 2.105 3.080 nonbonded pdb=" O06 PGV P 103 " pdb=" O12 PGV P 103 " model vdw 2.109 3.040 nonbonded pdb=" NE2 HIS C 297 " pdb="FE HEM C 405 " model vdw 2.114 3.080 ... (remaining 214338 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: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 7 through 55) selection = (chain '2' and resid 7 through 55) selection = (chain '4' and resid 7 through 55) selection = (chain '6' and resid 7 through 55) selection = (chain '8' and resid 7 through 55) selection = (chain 'B' and resid 7 through 55) selection = (chain 'E' and resid 7 through 55) selection = (chain 'G' and resid 7 through 55) selection = (chain 'I' and resid 7 through 55) selection = (chain 'K' and resid 7 through 55) selection = (chain 'O' and resid 7 through 55) selection = (chain 'Q' and resid 7 through 55) selection = (chain 'S' and resid 7 through 55) selection = (chain 'U' and resid 7 through 55) selection = (chain 'W' and resid 7 through 55) } ncs_group { reference = (chain '1' and resid 7 through 41) selection = (chain '3' and resid 7 through 41) selection = (chain '5' and resid 7 through 41) selection = (chain '7' and resid 7 through 41) selection = (chain '9' and resid 7 through 41) selection = (chain 'A' and resid 7 through 41) selection = (chain 'D' and resid 7 through 41) selection = (chain 'F' and resid 7 through 41) selection = (chain 'H' and resid 7 through 41) selection = (chain 'J' and resid 7 through 41) selection = (chain 'N' and resid 7 through 41) selection = (chain 'P' and resid 7 through 41) selection = (chain 'R' and resid 7 through 41) selection = (chain 'T' and resid 7 through 41) selection = (chain 'V' and resid 7 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 21.950 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.029 0.659 25026 Z= 2.286 Angle : 2.080 16.829 34760 Z= 0.863 Chirality : 0.397 5.589 3424 Planarity : 0.031 0.293 4222 Dihedral : 20.157 144.679 8435 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 0.66 % Allowed : 9.24 % Favored : 90.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: 2256 helix: 0.58 (0.12), residues: 1410 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 40 TYR 0.018 0.002 TYR C 156 PHE 0.025 0.002 PHE L 206 TRP 0.031 0.002 TRP D 38 HIS 0.007 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.01966 / 0.87 (24965) covalent geometry : angle 2.07962 / 0.86 (34760) hydrogen bonds : bond 0.10891 / 7.18 ( 1246) hydrogen bonds : angle 5.24901 / 3.87 ( 3663) Misc. bond : bond 0.43468 / 28.13 ( 61) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 455 time to evaluate : 0.837 Fit side-chains REVERT: 0 19 ASN cc_start: 0.6837 (t0) cc_final: 0.6613 (t0) REVERT: 3 22 MET cc_start: 0.8708 (mmm) cc_final: 0.8483 (mmp) REVERT: 4 27 ASP cc_start: 0.7372 (t0) cc_final: 0.7171 (t70) REVERT: 9 17 LEU cc_start: 0.8112 (tp) cc_final: 0.7724 (mm) REVERT: A 22 MET cc_start: 0.9140 (mmm) cc_final: 0.8900 (mmp) REVERT: D 9 ARG cc_start: 0.6433 (ttp-170) cc_final: 0.5951 (tmt170) REVERT: D 10 THR cc_start: 0.8295 (m) cc_final: 0.8083 (m) REVERT: G 31 LYS cc_start: 0.8370 (mttt) cc_final: 0.8160 (mttp) REVERT: J 4 ARG cc_start: 0.6410 (tpt-90) cc_final: 0.6183 (mtp180) REVERT: L 151 ASP cc_start: 0.8847 (m-30) cc_final: 0.8552 (m-30) REVERT: N 9 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7278 (ttm170) REVERT: S 19 ASN cc_start: 0.7880 (t0) cc_final: 0.7634 (t0) REVERT: C 223 GLU cc_start: 0.8303 (tt0) cc_final: 0.7995 (tt0) REVERT: X 8 PHE cc_start: 0.6827 (t80) cc_final: 0.6595 (t80) REVERT: Z 43 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (ttpp) outliers start: 13 outliers final: 6 residues processed: 466 average time/residue: 0.6008 time to fit residues: 327.1994 Evaluate side-chains 329 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 322 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN G 19 ASN I 19 ASN L 120 GLN M 572 GLN O 13 GLN Q 13 GLN S 22 GLN W 13 GLN C 56 ASN C 87 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100621 restraints weight = 31134.793| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.22 r_work: 0.2872 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.451 25026 Z= 0.178 Angle : 0.957 18.615 34760 Z= 0.344 Chirality : 0.042 0.212 3424 Planarity : 0.005 0.067 4222 Dihedral : 20.663 179.148 4444 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.59 % Allowed : 14.12 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.17), residues: 2256 helix: 2.13 (0.13), residues: 1419 sheet: None (None), residues: 0 loop : -1.00 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 9 40 TYR 0.013 0.002 TYR C 230 PHE 0.016 0.001 PHE C 39 TRP 0.015 0.001 TRP K 50 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.18 (24965) covalent geometry : angle 0.95703 / 0.34 (34760) hydrogen bonds : bond 0.04476 / 3.01 ( 1246) hydrogen bonds : angle 4.16852 / 3.06 ( 3663) Misc. bond : bond 0.10799 / 7.61 ( 61) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7954 (tp) cc_final: 0.7734 (mp) REVERT: 4 27 ASP cc_start: 0.7974 (t0) cc_final: 0.7667 (t70) REVERT: 6 17 LEU cc_start: 0.8116 (mt) cc_final: 0.7901 (mt) REVERT: 9 17 LEU cc_start: 0.8373 (tp) cc_final: 0.7886 (mp) REVERT: D 7 GLU cc_start: 0.7096 (tp30) cc_final: 0.6796 (mm-30) REVERT: D 9 ARG cc_start: 0.7106 (ttp-170) cc_final: 0.6030 (tmt170) REVERT: D 10 THR cc_start: 0.8471 (m) cc_final: 0.8188 (m) REVERT: G 31 LYS cc_start: 0.8633 (mttt) cc_final: 0.8252 (mtpp) REVERT: K 27 ASP cc_start: 0.8239 (t0) cc_final: 0.8014 (t0) REVERT: L 41 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: L 151 ASP cc_start: 0.9219 (m-30) cc_final: 0.8847 (m-30) REVERT: M 348 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: N 9 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7590 (ttm170) REVERT: P 38 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8638 (t60) REVERT: U 55 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: W 8 ASP cc_start: 0.7206 (p0) cc_final: 0.6694 (t0) REVERT: W 9 LEU cc_start: 0.8046 (mt) cc_final: 0.7721 (mp) REVERT: W 17 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7631 (mm) REVERT: C 28 SER cc_start: 0.8239 (p) cc_final: 0.8019 (m) REVERT: C 73 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7605 (mp0) REVERT: C 145 MET cc_start: 0.8553 (mmt) cc_final: 0.7772 (mmt) REVERT: C 188 GLU cc_start: 0.8262 (mp0) cc_final: 0.8042 (pt0) REVERT: C 223 GLU cc_start: 0.8807 (tt0) cc_final: 0.8459 (tt0) REVERT: C 272 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Z 39 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8216 (tmt-80) REVERT: Z 43 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8562 (tttm) outliers start: 51 outliers final: 18 residues processed: 387 average time/residue: 0.5423 time to fit residues: 247.6202 Evaluate side-chains 345 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 320 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 191 optimal weight: 0.4980 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 2 22 GLN 4 22 GLN 5 37 ASN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN E 13 GLN I 19 ASN L 120 GLN M 369 GLN W 13 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104773 restraints weight = 31257.543| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.23 r_work: 0.2917 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.368 25026 Z= 0.136 Angle : 0.714 14.100 34760 Z= 0.291 Chirality : 0.038 0.175 3424 Planarity : 0.004 0.048 4222 Dihedral : 18.301 179.993 4440 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.18 % Allowed : 15.95 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.17), residues: 2256 helix: 2.58 (0.13), residues: 1433 sheet: None (None), residues: 0 loop : -0.87 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 4 TYR 0.013 0.001 TYR C 230 PHE 0.025 0.001 PHE X 8 TRP 0.015 0.001 TRP M 575 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (24965) covalent geometry : angle 0.71414 / 0.29 (34760) hydrogen bonds : bond 0.04007 / 2.70 ( 1246) hydrogen bonds : angle 3.82799 / 2.81 ( 3663) Misc. bond : bond 0.06637 / 4.58 ( 61) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 364 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.8494 (t70) cc_final: 0.8160 (t0) REVERT: 3 7 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6949 (mp0) REVERT: 4 19 ASN cc_start: 0.7302 (t0) cc_final: 0.7036 (t0) REVERT: 4 27 ASP cc_start: 0.7987 (t0) cc_final: 0.7709 (t70) REVERT: 6 15 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7836 (mmtm) REVERT: 6 17 LEU cc_start: 0.8074 (mt) cc_final: 0.7856 (mt) REVERT: 8 20 ASN cc_start: 0.8283 (t0) cc_final: 0.7867 (m-40) REVERT: 8 38 ILE cc_start: 0.8716 (mm) cc_final: 0.8475 (mm) REVERT: 9 17 LEU cc_start: 0.8402 (tp) cc_final: 0.7912 (mp) REVERT: D 9 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.5913 (tmt170) REVERT: G 31 LYS cc_start: 0.8617 (mttt) cc_final: 0.8333 (mttp) REVERT: I 32 THR cc_start: 0.9058 (m) cc_final: 0.8770 (m) REVERT: J 9 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7336 (ptt90) REVERT: K 31 LYS cc_start: 0.8928 (mttt) cc_final: 0.8710 (mttt) REVERT: L 41 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: L 151 ASP cc_start: 0.9185 (m-30) cc_final: 0.8792 (m-30) REVERT: M 348 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: N 9 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7413 (ttm170) REVERT: Q 55 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7294 (mtp180) REVERT: U 8 ASP cc_start: 0.7446 (p0) cc_final: 0.7104 (p0) REVERT: U 13 GLN cc_start: 0.8496 (tp40) cc_final: 0.8236 (tp40) REVERT: W 8 ASP cc_start: 0.7298 (p0) cc_final: 0.6782 (t0) REVERT: W 9 LEU cc_start: 0.7973 (mt) cc_final: 0.7737 (mp) REVERT: C 17 ARG cc_start: 0.7324 (tpt170) cc_final: 0.6271 (tpp80) REVERT: C 28 SER cc_start: 0.8220 (p) cc_final: 0.7986 (m) REVERT: C 31 MET cc_start: 0.6982 (ttm) cc_final: 0.6538 (ttt) REVERT: C 223 GLU cc_start: 0.8799 (tt0) cc_final: 0.8421 (tt0) REVERT: C 272 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: Z 43 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8385 (tttm) REVERT: Z 56 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7552 (mmtt) outliers start: 43 outliers final: 16 residues processed: 384 average time/residue: 0.5488 time to fit residues: 248.2332 Evaluate side-chains 342 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 9 residue 10 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 168 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN W 13 GLN C 126 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100182 restraints weight = 31280.960| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.23 r_work: 0.2853 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.367 25026 Z= 0.154 Angle : 0.735 14.513 34760 Z= 0.298 Chirality : 0.039 0.214 3424 Planarity : 0.004 0.050 4222 Dihedral : 17.495 179.952 4436 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.74 % Allowed : 16.25 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.17), residues: 2256 helix: 2.59 (0.13), residues: 1439 sheet: None (None), residues: 0 loop : -0.74 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 55 TYR 0.015 0.002 TYR C 230 PHE 0.022 0.001 PHE X 8 TRP 0.013 0.001 TRP T 38 HIS 0.007 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 (24965) covalent geometry : angle 0.73504 / 0.30 (34760) hydrogen bonds : bond 0.04185 / 2.82 ( 1246) hydrogen bonds : angle 3.82541 / 2.80 ( 3663) Misc. bond : bond 0.07259 / 5.03 ( 61) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7682 (mp) REVERT: 0 27 ASP cc_start: 0.8523 (t70) cc_final: 0.8155 (t0) REVERT: 4 27 ASP cc_start: 0.8015 (t0) cc_final: 0.7719 (t70) REVERT: 6 17 LEU cc_start: 0.8090 (mt) cc_final: 0.7860 (mt) REVERT: 8 20 ASN cc_start: 0.8410 (t0) cc_final: 0.7858 (m-40) REVERT: 9 17 LEU cc_start: 0.8437 (tp) cc_final: 0.8125 (mt) REVERT: 9 22 MET cc_start: 0.9010 (mmm) cc_final: 0.8756 (mmm) REVERT: B 9 LEU cc_start: 0.8161 (mm) cc_final: 0.7603 (mp) REVERT: B 15 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7916 (mttp) REVERT: D 7 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: D 9 ARG cc_start: 0.7034 (ttp-170) cc_final: 0.6074 (tmt170) REVERT: G 31 LYS cc_start: 0.8629 (mttt) cc_final: 0.8370 (mttp) REVERT: I 31 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8646 (mtmm) REVERT: J 9 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7315 (ptt-90) REVERT: J 22 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7520 (mpm) REVERT: K 31 LYS cc_start: 0.9015 (mttt) cc_final: 0.8782 (mttp) REVERT: L 151 ASP cc_start: 0.9201 (m-30) cc_final: 0.8828 (m-30) REVERT: L 181 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.5281 (t-100) REVERT: M 348 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: N 9 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7684 (ttm170) REVERT: P 9 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.8121 (ttp-110) REVERT: Q 55 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7327 (mtp180) REVERT: U 8 ASP cc_start: 0.7501 (p0) cc_final: 0.7276 (p0) REVERT: U 13 GLN cc_start: 0.8479 (tp40) cc_final: 0.8211 (tp40) REVERT: W 8 ASP cc_start: 0.7448 (p0) cc_final: 0.6874 (t0) REVERT: W 9 LEU cc_start: 0.8038 (mt) cc_final: 0.7821 (mp) REVERT: C 17 ARG cc_start: 0.7369 (tpt170) cc_final: 0.6288 (tpp80) REVERT: C 31 MET cc_start: 0.7086 (ttm) cc_final: 0.6883 (ttm) REVERT: C 145 MET cc_start: 0.8652 (mmt) cc_final: 0.7614 (mmt) REVERT: C 223 GLU cc_start: 0.8819 (tt0) cc_final: 0.8461 (tt0) REVERT: C 272 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: Z 43 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8478 (tttp) REVERT: Z 56 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7533 (mmtt) outliers start: 54 outliers final: 20 residues processed: 367 average time/residue: 0.5004 time to fit residues: 216.5611 Evaluate side-chains 340 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 313 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 13 GLN E 13 GLN I 19 ASN L 120 GLN M 414 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094273 restraints weight = 31294.558| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.05 r_work: 0.2815 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.447 25026 Z= 0.250 Angle : 0.881 16.874 34760 Z= 0.351 Chirality : 0.044 0.245 3424 Planarity : 0.005 0.056 4222 Dihedral : 17.517 179.837 4436 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 15.90 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.17), residues: 2256 helix: 2.27 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.79 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 8 55 TYR 0.020 0.002 TYR M 424 PHE 0.025 0.002 PHE X 8 TRP 0.017 0.002 TRP T 38 HIS 0.009 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.25 (24965) covalent geometry : angle 0.88077 / 0.35 (34760) hydrogen bonds : bond 0.04849 / 3.25 ( 1246) hydrogen bonds : angle 4.11121 / 3.00 ( 3663) Misc. bond : bond 0.08573 / 6.06 ( 61) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 319 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7700 (mp) REVERT: 0 27 ASP cc_start: 0.8545 (t70) cc_final: 0.8220 (t0) REVERT: 3 9 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6759 (ttp-110) REVERT: 6 17 LEU cc_start: 0.8343 (mt) cc_final: 0.8116 (mt) REVERT: 7 9 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6877 (ttt180) REVERT: 8 20 ASN cc_start: 0.8471 (t0) cc_final: 0.7962 (m-40) REVERT: 9 17 LEU cc_start: 0.8456 (tp) cc_final: 0.7969 (mp) REVERT: B 15 LYS cc_start: 0.8242 (ttmt) cc_final: 0.8024 (mttp) REVERT: B 31 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8647 (mmtt) REVERT: D 7 GLU cc_start: 0.7518 (tp30) cc_final: 0.6976 (mm-30) REVERT: D 9 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6853 (ttt-90) REVERT: G 31 LYS cc_start: 0.8687 (mttt) cc_final: 0.8480 (mttm) REVERT: J 22 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7630 (mpm) REVERT: M 348 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: N 9 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7578 (ttm170) REVERT: Q 55 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7368 (mtp180) REVERT: S 31 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8502 (mttt) REVERT: U 13 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: W 8 ASP cc_start: 0.7540 (p0) cc_final: 0.7067 (t0) REVERT: W 28 ILE cc_start: 0.8292 (mm) cc_final: 0.8056 (mt) REVERT: C 17 ARG cc_start: 0.7592 (tpt170) cc_final: 0.6444 (tpp80) REVERT: C 28 SER cc_start: 0.8365 (p) cc_final: 0.8055 (m) REVERT: C 31 MET cc_start: 0.7150 (ttm) cc_final: 0.6708 (ttt) REVERT: C 188 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: C 223 GLU cc_start: 0.8852 (tt0) cc_final: 0.8562 (tt0) REVERT: C 272 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: Z 43 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8456 (tttm) REVERT: Z 56 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7708 (mmtt) outliers start: 56 outliers final: 23 residues processed: 351 average time/residue: 0.6013 time to fit residues: 246.3470 Evaluate side-chains 328 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 38 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096650 restraints weight = 31397.774| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.21 r_work: 0.2839 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.393 25026 Z= 0.172 Angle : 0.763 15.496 34760 Z= 0.307 Chirality : 0.040 0.225 3424 Planarity : 0.005 0.051 4222 Dihedral : 17.085 179.912 4435 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.39 % Allowed : 16.56 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.17), residues: 2256 helix: 2.45 (0.13), residues: 1437 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 8 55 TYR 0.014 0.002 TYR C 230 PHE 0.025 0.001 PHE X 8 TRP 0.013 0.002 TRP T 38 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (24965) covalent geometry : angle 0.76311 / 0.31 (34760) hydrogen bonds : bond 0.04331 / 2.91 ( 1246) hydrogen bonds : angle 3.94018 / 2.88 ( 3663) Misc. bond : bond 0.07685 / 5.41 ( 61) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 323 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7723 (mp) REVERT: 0 27 ASP cc_start: 0.8615 (t70) cc_final: 0.8297 (t0) REVERT: 0 38 ILE cc_start: 0.8599 (mm) cc_final: 0.8271 (mt) REVERT: 3 9 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.6688 (ttt90) REVERT: 5 12 VAL cc_start: 0.8655 (t) cc_final: 0.8422 (t) REVERT: 6 17 LEU cc_start: 0.8380 (mt) cc_final: 0.8173 (mt) REVERT: 7 9 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6857 (ttt180) REVERT: 8 20 ASN cc_start: 0.8423 (t0) cc_final: 0.7960 (m-40) REVERT: 9 17 LEU cc_start: 0.8458 (tp) cc_final: 0.7992 (mp) REVERT: D 7 GLU cc_start: 0.7533 (tp30) cc_final: 0.6991 (mm-30) REVERT: D 9 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.6874 (ttt-90) REVERT: I 7 ASN cc_start: 0.7657 (p0) cc_final: 0.7375 (p0) REVERT: I 31 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8616 (mtmm) REVERT: J 22 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7717 (mpm) REVERT: M 348 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: M 505 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8815 (pt) REVERT: Q 55 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7269 (mtp180) REVERT: S 31 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8389 (mptt) REVERT: U 13 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8208 (tp40) REVERT: W 8 ASP cc_start: 0.7562 (p0) cc_final: 0.7114 (t0) REVERT: C 17 ARG cc_start: 0.7505 (tpt170) cc_final: 0.6381 (tpp80) REVERT: C 28 SER cc_start: 0.8380 (p) cc_final: 0.8067 (m) REVERT: C 223 GLU cc_start: 0.8870 (tt0) cc_final: 0.8526 (tt0) REVERT: C 272 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: Z 43 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (tttp) REVERT: Z 56 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7706 (mmtt) outliers start: 47 outliers final: 21 residues processed: 351 average time/residue: 0.5831 time to fit residues: 240.2103 Evaluate side-chains 335 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 119 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN 8 22 GLN B 13 GLN E 13 GLN I 19 ASN L 112 GLN L 120 GLN L 306 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094815 restraints weight = 30881.191| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.01 r_work: 0.2798 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.451 25026 Z= 0.218 Angle : 0.832 16.619 34760 Z= 0.331 Chirality : 0.042 0.226 3424 Planarity : 0.005 0.056 4222 Dihedral : 17.052 179.854 4435 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.64 % Allowed : 17.12 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.17), residues: 2256 helix: 2.33 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.77 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 8 55 TYR 0.017 0.002 TYR C 230 PHE 0.025 0.002 PHE X 8 TRP 0.015 0.002 TRP T 38 HIS 0.008 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 (24965) covalent geometry : angle 0.83188 / 0.33 (34760) hydrogen bonds : bond 0.04607 / 3.09 ( 1246) hydrogen bonds : angle 4.03269 / 2.94 ( 3663) Misc. bond : bond 0.07398 / 5.55 ( 61) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7702 (mp) REVERT: 0 27 ASP cc_start: 0.8535 (t70) cc_final: 0.8226 (t70) REVERT: 0 38 ILE cc_start: 0.8570 (mm) cc_final: 0.8244 (mt) REVERT: 2 7 ASN cc_start: 0.7080 (p0) cc_final: 0.6506 (p0) REVERT: 3 9 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.6884 (ttm110) REVERT: 4 34 TYR cc_start: 0.7983 (m-10) cc_final: 0.7716 (m-10) REVERT: 7 9 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6853 (ttt180) REVERT: 8 20 ASN cc_start: 0.8444 (t0) cc_final: 0.8006 (m-40) REVERT: 9 17 LEU cc_start: 0.8302 (tp) cc_final: 0.7818 (mp) REVERT: D 9 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.6792 (ttt-90) REVERT: I 7 ASN cc_start: 0.7788 (p0) cc_final: 0.7412 (p0) REVERT: I 31 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8562 (mtmm) REVERT: J 22 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7676 (mpm) REVERT: K 13 GLN cc_start: 0.7781 (tt0) cc_final: 0.7534 (tt0) REVERT: L 151 ASP cc_start: 0.9171 (m-30) cc_final: 0.8799 (m-30) REVERT: L 181 TRP cc_start: 0.7102 (OUTLIER) cc_final: 0.5597 (t-100) REVERT: M 348 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7700 (mm-30) REVERT: M 505 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8789 (pt) REVERT: P 38 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.8537 (t60) REVERT: Q 55 ARG cc_start: 0.7588 (ttm170) cc_final: 0.7291 (mtp180) REVERT: S 31 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8381 (mttt) REVERT: U 13 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8173 (tp40) REVERT: W 8 ASP cc_start: 0.7535 (p0) cc_final: 0.7142 (t0) REVERT: W 9 LEU cc_start: 0.7886 (mp) cc_final: 0.7641 (mt) REVERT: C 17 ARG cc_start: 0.7374 (tpt170) cc_final: 0.6192 (tpp80) REVERT: C 28 SER cc_start: 0.8261 (p) cc_final: 0.7968 (m) REVERT: C 106 MET cc_start: 0.7916 (ttm) cc_final: 0.7659 (ttm) REVERT: C 223 GLU cc_start: 0.8806 (tt0) cc_final: 0.8466 (tt0) REVERT: C 272 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: X 26 SER cc_start: 0.6362 (OUTLIER) cc_final: 0.5681 (p) REVERT: Z 43 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8558 (tttp) REVERT: Z 56 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7732 (mmtt) outliers start: 52 outliers final: 28 residues processed: 341 average time/residue: 0.5718 time to fit residues: 228.8372 Evaluate side-chains 335 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN Y 2 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097588 restraints weight = 30659.797| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.00 r_work: 0.2840 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.407 25026 Z= 0.168 Angle : 0.763 15.332 34760 Z= 0.307 Chirality : 0.040 0.207 3424 Planarity : 0.005 0.054 4222 Dihedral : 16.700 179.889 4435 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.59 % Allowed : 17.62 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.17), residues: 2256 helix: 2.48 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 8 55 TYR 0.015 0.002 TYR C 133 PHE 0.027 0.001 PHE X 8 TRP 0.017 0.002 TRP C 41 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (24965) covalent geometry : angle 0.76267 / 0.31 (34760) hydrogen bonds : bond 0.04311 / 2.89 ( 1246) hydrogen bonds : angle 3.91624 / 2.86 ( 3663) Misc. bond : bond 0.06696 / 4.98 ( 61) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7755 (mp) REVERT: 0 27 ASP cc_start: 0.8511 (t70) cc_final: 0.8150 (t70) REVERT: 0 38 ILE cc_start: 0.8590 (mm) cc_final: 0.8258 (mt) REVERT: 2 7 ASN cc_start: 0.7155 (p0) cc_final: 0.6599 (p0) REVERT: 3 9 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.6547 (ttt90) REVERT: 5 12 VAL cc_start: 0.8596 (t) cc_final: 0.8337 (t) REVERT: 7 9 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6832 (ttt180) REVERT: 8 20 ASN cc_start: 0.8388 (t0) cc_final: 0.7925 (m-40) REVERT: 9 17 LEU cc_start: 0.8289 (tp) cc_final: 0.7907 (mm) REVERT: D 7 GLU cc_start: 0.7450 (tp30) cc_final: 0.6874 (mm-30) REVERT: D 9 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6644 (ttt-90) REVERT: F 9 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7479 (ttp80) REVERT: I 31 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8619 (mtmm) REVERT: J 22 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7552 (mpm) REVERT: K 13 GLN cc_start: 0.7760 (tt0) cc_final: 0.7531 (tt0) REVERT: L 151 ASP cc_start: 0.9162 (m-30) cc_final: 0.8812 (m-30) REVERT: M 348 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: M 505 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8788 (pt) REVERT: S 31 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8357 (mttt) REVERT: S 55 ARG cc_start: 0.7553 (mtp85) cc_final: 0.6559 (mtt-85) REVERT: U 13 GLN cc_start: 0.8454 (tp40) cc_final: 0.8180 (tp40) REVERT: V 11 SER cc_start: 0.8769 (m) cc_final: 0.8355 (p) REVERT: W 8 ASP cc_start: 0.7522 (p0) cc_final: 0.7155 (t0) REVERT: W 9 LEU cc_start: 0.7927 (mp) cc_final: 0.7686 (mt) REVERT: C 17 ARG cc_start: 0.7354 (tpt170) cc_final: 0.6263 (tpp80) REVERT: C 28 SER cc_start: 0.8300 (p) cc_final: 0.8010 (m) REVERT: C 31 MET cc_start: 0.7066 (ttm) cc_final: 0.6809 (ttm) REVERT: C 223 GLU cc_start: 0.8782 (tt0) cc_final: 0.8438 (tt0) REVERT: C 272 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: X 26 SER cc_start: 0.6370 (OUTLIER) cc_final: 0.5782 (p) REVERT: Z 43 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8452 (tttp) REVERT: Z 56 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7753 (mmtt) outliers start: 51 outliers final: 31 residues processed: 360 average time/residue: 0.5550 time to fit residues: 234.8347 Evaluate side-chains 346 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 28 optimal weight: 0.0270 chunk 119 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 171 optimal weight: 0.3980 chunk 190 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN W 22 GLN Y 2 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.097790 restraints weight = 30816.243| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.11 r_work: 0.2826 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.414 25026 Z= 0.164 Angle : 0.754 15.418 34760 Z= 0.306 Chirality : 0.039 0.192 3424 Planarity : 0.005 0.056 4222 Dihedral : 16.457 179.910 4435 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.59 % Allowed : 17.67 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.17), residues: 2256 helix: 2.51 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.72 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 8 55 TYR 0.015 0.002 TYR C 133 PHE 0.027 0.001 PHE X 8 TRP 0.019 0.001 TRP C 41 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (24965) covalent geometry : angle 0.75400 / 0.31 (34760) hydrogen bonds : bond 0.04288 / 2.88 ( 1246) hydrogen bonds : angle 3.88363 / 2.83 ( 3663) Misc. bond : bond 0.06658 / 4.95 ( 61) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7750 (mp) REVERT: 0 27 ASP cc_start: 0.8505 (t70) cc_final: 0.8240 (t0) REVERT: 0 38 ILE cc_start: 0.8591 (mm) cc_final: 0.8257 (mt) REVERT: 2 7 ASN cc_start: 0.7265 (p0) cc_final: 0.6685 (p0) REVERT: 3 9 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.6536 (ttt90) REVERT: 4 34 TYR cc_start: 0.7939 (m-10) cc_final: 0.7684 (m-10) REVERT: 5 12 VAL cc_start: 0.8574 (t) cc_final: 0.8284 (t) REVERT: 7 9 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6817 (ttt180) REVERT: 8 20 ASN cc_start: 0.8339 (t0) cc_final: 0.7879 (m-40) REVERT: 9 17 LEU cc_start: 0.8366 (tp) cc_final: 0.7939 (mm) REVERT: D 9 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6705 (ttt-90) REVERT: F 9 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7477 (ttp80) REVERT: I 31 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8616 (mtmm) REVERT: J 22 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7662 (mpm) REVERT: K 13 GLN cc_start: 0.7798 (tt0) cc_final: 0.7577 (tt0) REVERT: L 151 ASP cc_start: 0.9177 (m-30) cc_final: 0.8836 (m-30) REVERT: M 348 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: M 505 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8782 (pt) REVERT: S 55 ARG cc_start: 0.7573 (mtp85) cc_final: 0.6580 (mtt-85) REVERT: U 13 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8191 (tp40) REVERT: U 55 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: V 11 SER cc_start: 0.8724 (m) cc_final: 0.8349 (p) REVERT: C 17 ARG cc_start: 0.7338 (tpt170) cc_final: 0.6246 (tpp80) REVERT: C 28 SER cc_start: 0.8361 (p) cc_final: 0.8067 (m) REVERT: C 31 MET cc_start: 0.7029 (ttm) cc_final: 0.6807 (ttm) REVERT: C 106 MET cc_start: 0.7917 (ttm) cc_final: 0.7594 (ttm) REVERT: C 223 GLU cc_start: 0.8808 (tt0) cc_final: 0.8463 (tt0) REVERT: C 272 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: X 26 SER cc_start: 0.6310 (OUTLIER) cc_final: 0.5736 (p) REVERT: Z 43 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8407 (tttp) REVERT: Z 56 LYS cc_start: 0.7975 (mmtm) cc_final: 0.7714 (mmtt) outliers start: 51 outliers final: 36 residues processed: 343 average time/residue: 0.5316 time to fit residues: 214.5345 Evaluate side-chains 347 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 11 MET Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 127 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN Y 2 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097157 restraints weight = 30809.000| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.02 r_work: 0.2829 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.430 25026 Z= 0.177 Angle : 0.776 15.958 34760 Z= 0.314 Chirality : 0.040 0.208 3424 Planarity : 0.005 0.055 4222 Dihedral : 16.427 179.909 4435 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 17.98 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.17), residues: 2256 helix: 2.46 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.72 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 8 55 TYR 0.016 0.002 TYR U 34 PHE 0.026 0.002 PHE X 8 TRP 0.022 0.002 TRP C 41 HIS 0.007 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (24965) covalent geometry : angle 0.77558 / 0.31 (34760) hydrogen bonds : bond 0.04385 / 2.94 ( 1246) hydrogen bonds : angle 3.91093 / 2.85 ( 3663) Misc. bond : bond 0.06976 / 5.17 ( 61) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: 0 7 ASN cc_start: 0.6950 (p0) cc_final: 0.6237 (t0) REVERT: 0 9 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7796 (mp) REVERT: 0 27 ASP cc_start: 0.8484 (t70) cc_final: 0.8228 (t0) REVERT: 0 38 ILE cc_start: 0.8660 (mm) cc_final: 0.8340 (mt) REVERT: 2 7 ASN cc_start: 0.7298 (p0) cc_final: 0.6686 (p0) REVERT: 3 9 ARG cc_start: 0.7342 (ttp-170) cc_final: 0.6744 (ttm110) REVERT: 4 34 TYR cc_start: 0.7925 (m-10) cc_final: 0.7663 (m-10) REVERT: 5 12 VAL cc_start: 0.8553 (t) cc_final: 0.8261 (t) REVERT: 7 9 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6809 (ttt180) REVERT: 8 20 ASN cc_start: 0.8313 (t0) cc_final: 0.7869 (m-40) REVERT: 9 17 LEU cc_start: 0.8379 (tp) cc_final: 0.7946 (mm) REVERT: D 9 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6725 (ttt-90) REVERT: F 9 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7462 (ttp80) REVERT: H 4 ARG cc_start: 0.6050 (ttp-170) cc_final: 0.5660 (ttm170) REVERT: I 31 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8608 (mtmm) REVERT: J 9 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7370 (ptt90) REVERT: J 22 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7551 (mpm) REVERT: K 13 GLN cc_start: 0.7818 (tt0) cc_final: 0.7573 (tt0) REVERT: K 55 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7168 (ttm170) REVERT: L 151 ASP cc_start: 0.9176 (m-30) cc_final: 0.8869 (m-30) REVERT: M 348 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: M 505 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8796 (pt) REVERT: S 31 LYS cc_start: 0.8693 (mppt) cc_final: 0.8263 (mptt) REVERT: S 55 ARG cc_start: 0.7589 (mtp85) cc_final: 0.6596 (mtt-85) REVERT: U 13 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: U 55 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7538 (mtm-85) REVERT: V 11 SER cc_start: 0.8718 (m) cc_final: 0.8341 (p) REVERT: W 8 ASP cc_start: 0.7488 (p0) cc_final: 0.7155 (t0) REVERT: C 17 ARG cc_start: 0.7431 (tpt170) cc_final: 0.6330 (tpp80) REVERT: C 28 SER cc_start: 0.8327 (p) cc_final: 0.8014 (m) REVERT: C 31 MET cc_start: 0.7012 (ttm) cc_final: 0.6793 (ttm) REVERT: C 106 MET cc_start: 0.7896 (ttm) cc_final: 0.7594 (ttm) REVERT: C 223 GLU cc_start: 0.8787 (tt0) cc_final: 0.8462 (tt0) REVERT: C 236 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6014 (mtm) REVERT: C 272 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: X 26 SER cc_start: 0.6299 (OUTLIER) cc_final: 0.5763 (p) REVERT: Y 2 ASN cc_start: 0.7518 (t0) cc_final: 0.7286 (t0) REVERT: Z 43 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8397 (tttp) REVERT: Z 56 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7717 (mmtt) outliers start: 51 outliers final: 37 residues processed: 344 average time/residue: 0.5384 time to fit residues: 217.6194 Evaluate side-chains 348 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 290 LYS Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 11 MET Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 151 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 GLN 4 22 GLN B 13 GLN E 13 GLN I 19 ASN L 115 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100212 restraints weight = 30700.024| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.11 r_work: 0.2878 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.373 25026 Z= 0.132 Angle : 0.704 14.400 34760 Z= 0.291 Chirality : 0.038 0.161 3424 Planarity : 0.004 0.054 4222 Dihedral : 16.085 179.971 4435 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.18 % Allowed : 18.59 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.17), residues: 2256 helix: 2.67 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.67 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 8 55 TYR 0.016 0.002 TYR 8 34 PHE 0.026 0.001 PHE X 8 TRP 0.023 0.001 TRP C 41 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (24965) covalent geometry : angle 0.70412 / 0.29 (34760) hydrogen bonds : bond 0.04032 / 2.71 ( 1246) hydrogen bonds : angle 3.76605 / 2.75 ( 3663) Misc. bond : bond 0.06007 / 4.44 ( 61) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7890.84 seconds wall clock time: 135 minutes 24.97 seconds (8124.97 seconds total)