Starting phenix.real_space_refine on Sun Jul 5 04:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc8_36151/07_2026/8jc8_36151.cif" } resolution = 3.11 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14182 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 15 9.91 5 Mg 30 5.21 5 S 45 5.16 5 C 10283 2.51 5 N 1949 2.21 5 O 2134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 14456 Number of models: 1 Model: "" Number of chains: 60 Chain: "2" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "6" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "7" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "8" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "B" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} bond proxies already assigned to first conformer: 435 Chain: "E" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 326 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "F" Number of atoms: 433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} bond proxies already assigned to first conformer: 435 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} bond proxies already assigned to first conformer: 435 Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "N" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "P" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "R" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "T" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 360 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "V" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "Z" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "1" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "Y" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "X" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'8K6': 2, 'BCL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'8K6': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "J" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'8K6': 2, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'8K6': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'8K6': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 14456 At special positions: 0 Unit cell: (123.71, 123.71, 76.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 15 19.99 S 45 16.00 Mg 30 11.99 O 2134 8.00 N 1949 7.00 C 10283 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 435.1 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain '2' and resid 10 through 43 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.618A pdb=" N ILE 3 14 " --> pdb=" O ILE 3 11 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 42 removed outlier: 3.601A pdb=" N THR 3 42 " --> pdb=" O ILE 3 38 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 43 Processing helix chain '5' and resid 7 through 14 removed outlier: 3.588A pdb=" N LYS 5 10 " --> pdb=" O ASN 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 16 through 42 removed outlier: 3.562A pdb=" N THR 5 42 " --> pdb=" O ILE 5 38 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 43 Processing helix chain '7' and resid 7 through 14 Processing helix chain '7' and resid 16 through 42 removed outlier: 3.575A pdb=" N THR 7 42 " --> pdb=" O ILE 7 38 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 43 Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 16 through 42 removed outlier: 3.571A pdb=" N THR A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'D' and resid 7 through 14 Processing helix chain 'D' and resid 16 through 41 Processing helix chain 'E' and resid 10 through 43 Processing helix chain 'F' and resid 7 through 14 Processing helix chain 'F' and resid 16 through 41 Processing helix chain 'G' and resid 10 through 43 Processing helix chain 'I' and resid 7 through 14 removed outlier: 3.567A pdb=" N LYS I 10 " --> pdb=" O ASN I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 41 Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 16 through 42 removed outlier: 3.524A pdb=" N THR K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 43 Processing helix chain 'O' and resid 7 through 14 Processing helix chain 'O' and resid 16 through 42 removed outlier: 3.614A pdb=" N THR O 42 " --> pdb=" O ILE O 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 Processing helix chain 'Q' and resid 7 through 14 Processing helix chain 'Q' and resid 16 through 41 Processing helix chain 'R' and resid 10 through 43 Processing helix chain 'S' and resid 7 through 14 removed outlier: 3.540A pdb=" N ILE S 14 " --> pdb=" O ILE S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 42 Processing helix chain 'T' and resid 10 through 43 Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.516A pdb=" N LYS U 10 " --> pdb=" O ASN U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 41 Processing helix chain 'V' and resid 10 through 43 Processing helix chain 'W' and resid 7 through 14 Processing helix chain 'W' and resid 16 through 42 removed outlier: 3.581A pdb=" N THR W 42 " --> pdb=" O ILE W 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 43 Processing helix chain '1' and resid 7 through 14 removed outlier: 3.615A pdb=" N LYS 1 10 " --> pdb=" O ASN 1 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE 1 14 " --> pdb=" O ILE 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 16 through 39 removed outlier: 3.568A pdb=" N VAL 1 39 " --> pdb=" O ILE 1 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 14 removed outlier: 3.520A pdb=" N LYS Y 10 " --> pdb=" O ASN Y 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE Y 14 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 39 removed outlier: 3.627A pdb=" N VAL Y 39 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 43 841 hydrogen bonds defined for protein. 2322 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: 1.64 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 4068 1.36 - 1.54: 10409 1.54 - 1.71: 297 1.71 - 1.88: 90 1.88 - 2.05: 120 Bond restraints: 14984 Sorted by residual: bond pdb=" NA BCL Y 103 " pdb="MG BCL Y 103 " ideal model delta sigma weight residual 2.170 1.992 0.178 2.40e-02 1.74e+03 5.49e+01 bond pdb=" NA BCL U 102 " pdb="MG BCL U 102 " ideal model delta sigma weight residual 2.170 1.993 0.177 2.40e-02 1.74e+03 5.44e+01 bond pdb=" NA BCL I 102 " pdb="MG BCL I 102 " ideal model delta sigma weight residual 2.170 1.994 0.176 2.40e-02 1.74e+03 5.37e+01 bond pdb=" NA BCL D 102 " pdb="MG BCL D 102 " ideal model delta sigma weight residual 2.170 1.995 0.175 2.40e-02 1.74e+03 5.33e+01 bond pdb=" NA BCL 5 102 " pdb="MG BCL 5 102 " ideal model delta sigma weight residual 2.170 1.995 0.175 2.40e-02 1.74e+03 5.33e+01 ... (remaining 14979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 19141 3.77 - 7.55: 1394 7.55 - 11.32: 164 11.32 - 15.10: 30 15.10 - 18.87: 14 Bond angle restraints: 20743 Sorted by residual: angle pdb=" CA ASP Y 49 " pdb=" CB ASP Y 49 " pdb=" CG ASP Y 49 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" NA BCL S 102 " pdb="MG BCL S 102 " pdb=" NC BCL S 102 " ideal model delta sigma weight residual 160.52 179.39 -18.87 2.84e+00 1.24e-01 4.41e+01 angle pdb=" NA BCL I 102 " pdb="MG BCL I 102 " pdb=" NC BCL I 102 " ideal model delta sigma weight residual 160.52 179.30 -18.79 2.84e+00 1.24e-01 4.37e+01 angle pdb=" NA BCL U 102 " pdb="MG BCL U 102 " pdb=" NC BCL U 102 " ideal model delta sigma weight residual 160.52 179.17 -18.66 2.84e+00 1.24e-01 4.31e+01 angle pdb=" NA BCL 5 102 " pdb="MG BCL 5 102 " pdb=" NC BCL 5 102 " ideal model delta sigma weight residual 160.52 178.99 -18.48 2.84e+00 1.24e-01 4.23e+01 ... (remaining 20738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 7571 35.82 - 71.63: 371 71.63 - 107.45: 33 107.45 - 143.26: 0 143.26 - 179.08: 4 Dihedral angle restraints: 7979 sinusoidal: 3831 harmonic: 4148 Sorted by residual: dihedral pdb=" CBD BCL N 102 " pdb=" CGD BCL N 102 " pdb=" O2D BCL N 102 " pdb=" CED BCL N 102 " ideal model delta sinusoidal sigma weight residual -180.00 -95.81 -84.19 1 5.00e+00 4.00e-02 3.45e+02 dihedral pdb=" C1 BCL Z 101 " pdb=" C2 BCL Z 101 " pdb=" C3 BCL Z 101 " pdb=" C5 BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.92 179.08 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL X 102 " pdb=" C2 BCL X 102 " pdb=" C3 BCL X 102 " pdb=" C5 BCL X 102 " ideal model delta sinusoidal sigma weight residual 180.00 1.07 178.93 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 7976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1894 0.080 - 0.160: 193 0.160 - 0.239: 35 0.239 - 0.319: 7 0.319 - 0.399: 11 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CBD BCL T 101 " pdb=" CAD BCL T 101 " pdb=" CGD BCL T 101 " pdb=" CHA BCL T 101 " both_signs ideal model delta sigma weight residual False 2.62 2.22 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CBD BCL X 102 " pdb=" CAD BCL X 102 " pdb=" CGD BCL X 102 " pdb=" CHA BCL X 102 " both_signs ideal model delta sigma weight residual False 2.62 2.23 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CBD BCL 6 102 " pdb=" CAD BCL 6 102 " pdb=" CGD BCL 6 102 " pdb=" CHA BCL 6 102 " both_signs ideal model delta sigma weight residual False 2.62 2.24 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2137 not shown) Planarity restraints: 2491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL P 101 " 0.374 3.00e-02 1.11e+03 3.07e-01 5.22e+02 pdb=" CBA BCL P 101 " 0.162 3.00e-02 1.11e+03 pdb=" CGA BCL P 101 " -0.080 3.00e-02 1.11e+03 pdb=" O1A BCL P 101 " 0.082 3.00e-02 1.11e+03 pdb=" O2A BCL P 101 " -0.539 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " 0.349 3.00e-02 1.11e+03 2.86e-01 4.53e+02 pdb=" CBA BCL 2 101 " 0.175 3.00e-02 1.11e+03 pdb=" CGA BCL 2 101 " -0.080 3.00e-02 1.11e+03 pdb=" O1A BCL 2 101 " 0.052 3.00e-02 1.11e+03 pdb=" O2A BCL 2 101 " -0.496 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL U 102 " 0.348 3.00e-02 1.11e+03 2.82e-01 4.43e+02 pdb=" CBA BCL U 102 " 0.196 3.00e-02 1.11e+03 pdb=" CGA BCL U 102 " -0.089 3.00e-02 1.11e+03 pdb=" O1A BCL U 102 " 0.025 3.00e-02 1.11e+03 pdb=" O2A BCL U 102 " -0.480 3.00e-02 1.11e+03 ... (remaining 2488 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 63 2.57 - 3.15: 9778 3.15 - 3.73: 21218 3.73 - 4.32: 32652 4.32 - 4.90: 54936 Nonbonded interactions: 118647 Sorted by model distance: nonbonded pdb=" O TRP Y 46 " pdb="CA CA Y 102 " model vdw 1.981 3.250 nonbonded pdb=" OD1 ASP Y 49 " pdb="CA CA Y 102 " model vdw 2.087 3.250 nonbonded pdb=" OD1 ASP 1 49 " pdb="CA CA 1 101 " model vdw 2.154 3.250 nonbonded pdb=" OD2 ASP 6 11 " pdb=" NZ LYS 6 15 " model vdw 2.186 3.120 nonbonded pdb=" O TRP 1 46 " pdb="CA CA 1 101 " model vdw 2.216 3.250 ... (remaining 118642 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 '1' and (resid 6 through 40 or resid 42 through 57)) selection = (chain '3' and (resid 6 through 40 or resid 42 through 57)) selection = (chain '5' and (resid 6 through 40 or resid 42 through 57)) selection = (chain '7' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'A' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'D' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'F' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'I' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'K' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'O' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'Q' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'S' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'U' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'W' and (resid 6 through 40 or resid 42 through 57)) selection = (chain 'Y' and (resid 6 through 40 or resid 42 through 57)) } ncs_group { reference = (chain '2' and resid 9 through 46) selection = (chain '4' and resid 9 through 46) selection = (chain '6' and resid 9 through 46) selection = (chain '8' and resid 9 through 46) selection = (chain 'B' and resid 9 through 46) selection = (chain 'E' and resid 9 through 46) selection = (chain 'G' and resid 9 through 46) selection = (chain 'J' and resid 9 through 46) selection = (chain 'N' and resid 9 through 46) selection = (chain 'P' and resid 9 through 46) selection = (chain 'R' and resid 9 through 46) selection = (chain 'T' and resid 9 through 46) selection = (chain 'V' and resid 9 through 46) selection = (chain 'X' and resid 9 through 46) selection = (chain 'Z' and resid 9 through 46) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 : 0.027 0.566 15013 Z= 1.893 Angle : 1.920 18.870 20743 Z= 0.870 Chirality : 0.060 0.399 2140 Planarity : 0.030 0.307 2491 Dihedral : 19.245 179.077 5265 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.57 % Allowed : 0.65 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.89 % Cis-general : 0.00 % Twisted Proline : 4.44 % 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: 3.49 (0.24), residues: 1341 helix: 3.30 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -0.01 (0.35), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 43 TYR 0.010 0.001 TYR 1 55 PHE 0.018 0.001 PHE Z 17 TRP 0.024 0.001 TRP Z 28 HIS 0.010 0.001 HIS 1 36 Details of bonding type rmsd/Z covalent geometry : bond 0.02178 / 0.96 (14984) covalent geometry : angle 1.91991 / 0.87 (20743) hydrogen bonds : bond 0.12758 / 8.23 ( 841) hydrogen bonds : angle 3.76832 / 2.74 ( 2322) Misc. bond : bond 0.37134 / 23.08 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.393 Fit side-chains REVERT: A 37 MET cc_start: 0.7083 (mmt) cc_final: 0.6590 (mmt) REVERT: O 37 MET cc_start: 0.6564 (mmt) cc_final: 0.6322 (mmt) REVERT: 1 56 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: Y 56 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7640 (mt0) outliers start: 7 outliers final: 1 residues processed: 138 average time/residue: 0.0883 time to fit residues: 19.2795 Evaluate side-chains 125 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 56 GLN Chi-restraints excluded: chain Y residue 43 ASP Chi-restraints excluded: chain Y residue 56 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Y 7 ASN Y 28 GLN X 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105340 restraints weight = 33139.875| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.24 r_work: 0.2912 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15013 Z= 0.152 Angle : 0.675 15.121 20743 Z= 0.264 Chirality : 0.036 0.136 2140 Planarity : 0.004 0.052 2491 Dihedral : 15.014 179.993 2713 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.81 % Allowed : 3.23 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.20 (0.23), residues: 1341 helix: 3.97 (0.15), residues: 888 sheet: None (None), residues: 0 loop : 0.22 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 43 TYR 0.008 0.001 TYR Y 55 PHE 0.009 0.001 PHE 2 17 TRP 0.009 0.001 TRP J 45 HIS 0.004 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14984) covalent geometry : angle 0.67502 / 0.26 (20743) hydrogen bonds : bond 0.06482 / 4.27 ( 841) hydrogen bonds : angle 2.93213 / 2.15 ( 2322) Misc. bond : bond 0.00199 / 0.12 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.383 Fit side-chains REVERT: K 37 MET cc_start: 0.8015 (mmt) cc_final: 0.7679 (mmt) REVERT: Q 37 MET cc_start: 0.8091 (mmt) cc_final: 0.7742 (mmt) REVERT: W 37 MET cc_start: 0.8146 (mmt) cc_final: 0.7765 (mmt) outliers start: 10 outliers final: 7 residues processed: 126 average time/residue: 0.1019 time to fit residues: 20.0567 Evaluate side-chains 121 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 0.0030 chunk 93 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN 1 7 ASN Y 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.122982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.106924 restraints weight = 30918.131| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.19 r_work: 0.2934 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15013 Z= 0.130 Angle : 0.597 13.515 20743 Z= 0.236 Chirality : 0.035 0.129 2140 Planarity : 0.003 0.047 2491 Dihedral : 13.768 179.981 2705 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.65 % Allowed : 4.04 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.49 (0.23), residues: 1341 helix: 4.19 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.35 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 43 TYR 0.007 0.001 TYR 7 55 PHE 0.008 0.001 PHE T 21 TRP 0.007 0.001 TRP X 28 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14984) covalent geometry : angle 0.59747 / 0.24 (20743) hydrogen bonds : bond 0.05945 / 3.92 ( 841) hydrogen bonds : angle 2.79697 / 2.05 ( 2322) Misc. bond : bond 0.00105 / 0.07 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.445 Fit side-chains REVERT: A 37 MET cc_start: 0.8102 (mmt) cc_final: 0.7811 (mmt) outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.1056 time to fit residues: 19.4177 Evaluate side-chains 117 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108396 restraints weight = 26510.348| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.01 r_work: 0.2988 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15013 Z= 0.124 Angle : 0.582 12.657 20743 Z= 0.228 Chirality : 0.035 0.120 2140 Planarity : 0.003 0.044 2491 Dihedral : 13.560 179.972 2705 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.73 % Allowed : 4.69 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.64 (0.23), residues: 1341 helix: 4.30 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.43 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.006 0.001 TYR 7 55 PHE 0.008 0.001 PHE T 21 TRP 0.007 0.001 TRP 7 12 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14984) covalent geometry : angle 0.58206 / 0.23 (20743) hydrogen bonds : bond 0.05784 / 3.81 ( 841) hydrogen bonds : angle 2.75550 / 2.01 ( 2322) Misc. bond : bond 0.00101 / 0.07 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.348 Fit side-chains REVERT: Q 37 MET cc_start: 0.8051 (mmt) cc_final: 0.7648 (mmt) outliers start: 9 outliers final: 7 residues processed: 117 average time/residue: 0.0862 time to fit residues: 15.8096 Evaluate side-chains 114 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106132 restraints weight = 29841.700| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.21 r_work: 0.2941 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15013 Z= 0.130 Angle : 0.595 12.359 20743 Z= 0.233 Chirality : 0.035 0.130 2140 Planarity : 0.003 0.042 2491 Dihedral : 13.517 179.983 2705 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.73 % Allowed : 4.77 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.66 (0.22), residues: 1341 helix: 4.31 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.45 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.007 0.001 TYR 7 55 PHE 0.008 0.001 PHE G 21 TRP 0.007 0.001 TRP 7 12 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14984) covalent geometry : angle 0.59523 / 0.23 (20743) hydrogen bonds : bond 0.05973 / 3.94 ( 841) hydrogen bonds : angle 2.76091 / 2.02 ( 2322) Misc. bond : bond 0.00107 / 0.07 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.355 Fit side-chains REVERT: A 37 MET cc_start: 0.8195 (mmt) cc_final: 0.7889 (mmt) outliers start: 9 outliers final: 8 residues processed: 115 average time/residue: 0.0905 time to fit residues: 16.2808 Evaluate side-chains 115 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107710 restraints weight = 29971.980| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.12 r_work: 0.2957 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15013 Z= 0.125 Angle : 0.582 12.102 20743 Z= 0.228 Chirality : 0.035 0.124 2140 Planarity : 0.003 0.040 2491 Dihedral : 13.379 179.988 2705 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.81 % Allowed : 4.77 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.75 (0.22), residues: 1341 helix: 4.37 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.51 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.006 0.001 TYR 7 55 PHE 0.008 0.001 PHE T 21 TRP 0.007 0.001 TRP 7 12 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14984) covalent geometry : angle 0.58188 / 0.23 (20743) hydrogen bonds : bond 0.05783 / 3.81 ( 841) hydrogen bonds : angle 2.73657 / 2.00 ( 2322) Misc. bond : bond 0.00105 / 0.06 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.437 Fit side-chains REVERT: Q 37 MET cc_start: 0.8069 (mmt) cc_final: 0.7688 (mmt) outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 0.0944 time to fit residues: 16.8894 Evaluate side-chains 114 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 75 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 98 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.126718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110889 restraints weight = 28635.965| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.13 r_work: 0.2999 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15013 Z= 0.109 Angle : 0.545 11.704 20743 Z= 0.214 Chirality : 0.034 0.123 2140 Planarity : 0.003 0.039 2491 Dihedral : 13.076 179.979 2705 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.65 % Allowed : 5.42 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.92 (0.22), residues: 1341 helix: 4.48 (0.13), residues: 888 sheet: None (None), residues: 0 loop : 0.62 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 43 TYR 0.005 0.001 TYR 7 55 PHE 0.008 0.001 PHE V 21 TRP 0.006 0.001 TRP R 28 HIS 0.002 0.001 HIS Z 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (14984) covalent geometry : angle 0.54464 / 0.21 (20743) hydrogen bonds : bond 0.05015 / 3.31 ( 841) hydrogen bonds : angle 2.65350 / 1.93 ( 2322) Misc. bond : bond 0.00080 / 0.05 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.466 Fit side-chains REVERT: A 37 MET cc_start: 0.8093 (mmt) cc_final: 0.7811 (mmt) REVERT: W 37 MET cc_start: 0.8046 (mmt) cc_final: 0.7673 (mmt) outliers start: 8 outliers final: 8 residues processed: 119 average time/residue: 0.1019 time to fit residues: 19.0980 Evaluate side-chains 121 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 48 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain Y residue 43 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 ASN Q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105035 restraints weight = 29388.326| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.12 r_work: 0.2919 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15013 Z= 0.148 Angle : 0.638 12.249 20743 Z= 0.250 Chirality : 0.036 0.128 2140 Planarity : 0.003 0.038 2491 Dihedral : 13.485 179.994 2705 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.73 % Allowed : 5.42 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.71 (0.22), residues: 1341 helix: 4.33 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.51 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.007 0.001 TYR 7 55 PHE 0.009 0.001 PHE T 21 TRP 0.009 0.001 TRP I 12 HIS 0.004 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14984) covalent geometry : angle 0.63838 / 0.25 (20743) hydrogen bonds : bond 0.06455 / 4.26 ( 841) hydrogen bonds : angle 2.78942 / 2.04 ( 2322) Misc. bond : bond 0.00129 / 0.08 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.459 Fit side-chains REVERT: K 37 MET cc_start: 0.8188 (mmt) cc_final: 0.7981 (mmt) REVERT: O 37 MET cc_start: 0.8062 (mmt) cc_final: 0.7849 (mmt) REVERT: Q 37 MET cc_start: 0.8226 (mmt) cc_final: 0.7846 (mmt) outliers start: 9 outliers final: 9 residues processed: 113 average time/residue: 0.0935 time to fit residues: 16.6328 Evaluate side-chains 115 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 48 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain Y residue 43 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 7 ASN 5 7 ASN F 7 ASN Q 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.118533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.103191 restraints weight = 27253.876| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.08 r_work: 0.2894 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15013 Z= 0.161 Angle : 0.666 12.560 20743 Z= 0.262 Chirality : 0.037 0.130 2140 Planarity : 0.003 0.039 2491 Dihedral : 13.763 179.970 2705 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.97 % Allowed : 5.50 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.55 (0.22), residues: 1341 helix: 4.22 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.42 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.008 0.001 TYR 7 55 PHE 0.009 0.001 PHE T 21 TRP 0.009 0.001 TRP I 12 HIS 0.004 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (14984) covalent geometry : angle 0.66647 / 0.26 (20743) hydrogen bonds : bond 0.06986 / 4.60 ( 841) hydrogen bonds : angle 2.85668 / 2.09 ( 2322) Misc. bond : bond 0.00142 / 0.09 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.363 Fit side-chains REVERT: A 37 MET cc_start: 0.8309 (mmt) cc_final: 0.8001 (mmt) REVERT: O 37 MET cc_start: 0.8081 (mmt) cc_final: 0.7851 (mmt) REVERT: W 37 MET cc_start: 0.8188 (mmt) cc_final: 0.7914 (mmt) outliers start: 12 outliers final: 11 residues processed: 114 average time/residue: 0.0920 time to fit residues: 16.2390 Evaluate side-chains 116 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 48 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain Y residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 7 ASN F 7 ASN Q 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.123277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107930 restraints weight = 24518.765| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.00 r_work: 0.2961 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15013 Z= 0.130 Angle : 0.595 12.083 20743 Z= 0.235 Chirality : 0.035 0.127 2140 Planarity : 0.003 0.038 2491 Dihedral : 13.397 179.989 2705 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.81 % Allowed : 5.74 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.73 (0.23), residues: 1341 helix: 4.34 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.53 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.007 0.001 TYR 7 55 PHE 0.008 0.001 PHE R 21 TRP 0.007 0.001 TRP R 28 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14984) covalent geometry : angle 0.59467 / 0.23 (20743) hydrogen bonds : bond 0.05992 / 3.95 ( 841) hydrogen bonds : angle 2.75826 / 2.01 ( 2322) Misc. bond : bond 0.00102 / 0.06 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.332 Fit side-chains REVERT: A 37 MET cc_start: 0.8263 (mmt) cc_final: 0.7896 (mmt) REVERT: O 37 MET cc_start: 0.8044 (mmt) cc_final: 0.7786 (mmt) REVERT: Q 37 MET cc_start: 0.8110 (mmt) cc_final: 0.7718 (mmt) REVERT: W 37 MET cc_start: 0.8167 (mmt) cc_final: 0.7799 (mmt) outliers start: 10 outliers final: 10 residues processed: 109 average time/residue: 0.0947 time to fit residues: 16.3112 Evaluate side-chains 112 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 48 ASP Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain Y residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 97 optimal weight: 0.7980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 7 ASN F 7 ASN Q 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.126406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.111086 restraints weight = 23132.491| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 0.98 r_work: 0.3021 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15013 Z= 0.113 Angle : 0.556 11.580 20743 Z= 0.219 Chirality : 0.034 0.130 2140 Planarity : 0.003 0.038 2491 Dihedral : 13.185 179.986 2705 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.65 % Allowed : 5.90 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.90 (0.22), residues: 1341 helix: 4.46 (0.13), residues: 888 sheet: None (None), residues: 0 loop : 0.61 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.006 0.001 TYR 7 55 PHE 0.007 0.001 PHE P 21 TRP 0.007 0.001 TRP R 28 HIS 0.003 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14984) covalent geometry : angle 0.55569 / 0.22 (20743) hydrogen bonds : bond 0.05233 / 3.45 ( 841) hydrogen bonds : angle 2.67428 / 1.95 ( 2322) Misc. bond : bond 0.00089 / 0.06 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.54 seconds wall clock time: 53 minutes 54.61 seconds (3234.61 seconds total)