Starting phenix.real_space_refine on Sat May 24 12:52:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc8_36151/05_2025/8jc8_36151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc8_36151/05_2025/8jc8_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_36151/05_2025/8jc8_36151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc8_36151/05_2025/8jc8_36151.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc8_36151/05_2025/8jc8_36151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc8_36151/05_2025/8jc8_36151.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 106 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 177 Unusual residues: {' CA': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 8.41, per 1000 atoms: 0.58 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: 4.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.04 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: 3.35 Time building geometry restraints manager: 4.65 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 2.510 nonbonded pdb=" OD1 ASP Y 49 " pdb="CA CA Y 102 " model vdw 2.087 2.510 nonbonded pdb=" OD1 ASP 1 49 " pdb="CA CA 1 101 " model vdw 2.154 2.510 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 2.510 ... (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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.270 Find NCS groups from input model: 0.810 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 8.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.024 0.001 TRP Z 28 HIS 0.010 0.001 HIS 1 36 PHE 0.018 0.001 PHE Z 17 TYR 0.010 0.001 TYR 1 55 ARG 0.004 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.12758 ( 841) hydrogen bonds : angle 3.76832 ( 2322) covalent geometry : bond 0.02178 (14984) covalent geometry : angle 1.91991 (20743) Misc. bond : bond 0.37134 ( 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 : 1.294 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: 0.2294 time to fit residues: 49.0658 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 : 1.309 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3221 r_free = 0.3221 target = 0.120116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105489 restraints weight = 22599.245| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 0.91 r_work: 0.2934 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0954 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= 0.150 Angle : 0.669 14.640 20743 Z= 0.260 Chirality : 0.036 0.133 2140 Planarity : 0.004 0.052 2491 Dihedral : 15.036 179.976 2713 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.81 % Allowed : 3.31 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.23), residues: 1341 helix: 3.97 (0.15), residues: 888 sheet: None (None), residues: 0 loop : 0.28 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 28 HIS 0.004 0.001 HIS G 36 PHE 0.009 0.001 PHE 2 17 TYR 0.007 0.001 TYR Y 55 ARG 0.004 0.000 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.06464 ( 841) hydrogen bonds : angle 2.92836 ( 2322) covalent geometry : bond 0.00343 (14984) covalent geometry : angle 0.66948 (20743) Misc. bond : bond 0.00177 ( 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 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.428 Fit side-chains REVERT: K 37 MET cc_start: 0.7852 (mmt) cc_final: 0.7480 (mmt) REVERT: Q 37 MET cc_start: 0.7921 (mmt) cc_final: 0.7515 (mmt) REVERT: W 37 MET cc_start: 0.7942 (mmt) cc_final: 0.7474 (mmt) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.2378 time to fit residues: 45.1229 Evaluate side-chains 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 ASN Q 7 ASN Y 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.118451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.103925 restraints weight = 21426.850| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 0.90 r_work: 0.2901 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1248 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= 0.150 Angle : 0.647 13.867 20743 Z= 0.256 Chirality : 0.036 0.124 2140 Planarity : 0.004 0.048 2491 Dihedral : 14.059 179.984 2705 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.73 % Allowed : 3.64 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.23), residues: 1341 helix: 4.09 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.32 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 12 HIS 0.004 0.001 HIS G 36 PHE 0.009 0.001 PHE G 21 TYR 0.007 0.001 TYR Y 55 ARG 0.005 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06693 ( 841) hydrogen bonds : angle 2.87912 ( 2322) covalent geometry : bond 0.00342 (14984) covalent geometry : angle 0.64720 (20743) Misc. bond : bond 0.00118 ( 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 123 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.214 Fit side-chains REVERT: A 37 MET cc_start: 0.8032 (mmt) cc_final: 0.7691 (mmt) REVERT: O 37 MET cc_start: 0.7888 (mmt) cc_final: 0.7647 (mmt) outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.2301 time to fit residues: 42.8558 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 : 1.202 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 ASN Q 7 ASN 1 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.101160 restraints weight = 34201.390| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.32 r_work: 0.2860 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1376 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= 0.148 Angle : 0.636 13.010 20743 Z= 0.251 Chirality : 0.036 0.133 2140 Planarity : 0.003 0.045 2491 Dihedral : 13.904 179.996 2705 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.81 % Allowed : 4.28 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.23), residues: 1341 helix: 4.15 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.34 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 12 HIS 0.003 0.001 HIS G 36 PHE 0.008 0.001 PHE T 21 TYR 0.007 0.001 TYR 7 55 ARG 0.004 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06641 ( 841) hydrogen bonds : angle 2.86223 ( 2322) covalent geometry : bond 0.00336 (14984) covalent geometry : angle 0.63617 (20743) Misc. bond : bond 0.00123 ( 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 121 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.219 Fit side-chains REVERT: Q 37 MET cc_start: 0.8197 (mmt) cc_final: 0.7920 (mmt) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.2363 time to fit residues: 43.3878 Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Y residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3217 r_free = 0.3217 target = 0.119437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.103413 restraints weight = 31104.680| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.18 r_work: 0.2891 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15013 Z= 0.137 Angle : 0.610 12.720 20743 Z= 0.240 Chirality : 0.035 0.122 2140 Planarity : 0.003 0.043 2491 Dihedral : 13.767 179.995 2705 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.23), residues: 1341 helix: 4.23 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.39 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 12 HIS 0.003 0.001 HIS G 36 PHE 0.009 0.001 PHE G 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06310 ( 841) hydrogen bonds : angle 2.81647 ( 2322) covalent geometry : bond 0.00307 (14984) covalent geometry : angle 0.61018 (20743) Misc. bond : bond 0.00118 ( 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 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.249 Fit side-chains REVERT: A 37 MET cc_start: 0.8052 (mmt) cc_final: 0.7740 (mmt) REVERT: O 37 MET cc_start: 0.7981 (mmt) cc_final: 0.7728 (mmt) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.2457 time to fit residues: 43.7060 Evaluate side-chains 116 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3205 r_free = 0.3205 target = 0.118546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.104543 restraints weight = 19396.982| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.83 r_work: 0.2929 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15013 Z= 0.143 Angle : 0.628 12.622 20743 Z= 0.246 Chirality : 0.036 0.131 2140 Planarity : 0.003 0.041 2491 Dihedral : 13.754 179.996 2705 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.89 % Allowed : 4.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.23), residues: 1341 helix: 4.23 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.40 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 12 HIS 0.003 0.001 HIS G 36 PHE 0.008 0.001 PHE T 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06507 ( 841) hydrogen bonds : angle 2.83213 ( 2322) covalent geometry : bond 0.00323 (14984) covalent geometry : angle 0.62752 (20743) Misc. bond : bond 0.00120 ( 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 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.242 Fit side-chains REVERT: Q 37 MET cc_start: 0.8012 (mmt) cc_final: 0.7612 (mmt) outliers start: 11 outliers final: 11 residues processed: 116 average time/residue: 0.2481 time to fit residues: 44.5220 Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 103 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100421 restraints weight = 30616.329| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.11 r_work: 0.2859 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15013 Z= 0.176 Angle : 0.698 12.719 20743 Z= 0.274 Chirality : 0.037 0.131 2140 Planarity : 0.003 0.041 2491 Dihedral : 14.111 179.953 2705 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.89 % Allowed : 5.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.23), residues: 1341 helix: 4.10 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.29 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 12 HIS 0.004 0.001 HIS G 36 PHE 0.009 0.001 PHE T 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.07465 ( 841) hydrogen bonds : angle 2.93537 ( 2322) covalent geometry : bond 0.00418 (14984) covalent geometry : angle 0.69816 (20743) Misc. bond : bond 0.00144 ( 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 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.428 Fit side-chains REVERT: A 37 MET cc_start: 0.8136 (mmt) cc_final: 0.7832 (mmt) REVERT: O 37 MET cc_start: 0.8046 (mmt) cc_final: 0.7795 (mmt) REVERT: Q 37 MET cc_start: 0.8092 (mmt) cc_final: 0.7801 (mmt) outliers start: 11 outliers final: 11 residues processed: 116 average time/residue: 0.2310 time to fit residues: 41.7267 Evaluate side-chains 119 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3189 r_free = 0.3189 target = 0.117864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.103684 restraints weight = 17889.810| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 0.80 r_work: 0.2908 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 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 = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 15013 Z= 0.156 Angle : 0.654 12.733 20743 Z= 0.257 Chirality : 0.036 0.129 2140 Planarity : 0.003 0.040 2491 Dihedral : 13.850 179.969 2705 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.89 % Allowed : 5.50 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.23), residues: 1341 helix: 4.15 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.30 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS G 36 PHE 0.009 0.001 PHE R 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06911 ( 841) hydrogen bonds : angle 2.88066 ( 2322) covalent geometry : bond 0.00360 (14984) covalent geometry : angle 0.65368 (20743) Misc. bond : bond 0.00128 ( 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 117 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.266 Fit side-chains REVERT: A 37 MET cc_start: 0.8141 (mmt) cc_final: 0.7805 (mmt) REVERT: O 37 MET cc_start: 0.8047 (mmt) cc_final: 0.7789 (mmt) REVERT: W 37 MET cc_start: 0.8106 (mmt) cc_final: 0.7768 (mmt) outliers start: 11 outliers final: 11 residues processed: 113 average time/residue: 0.2371 time to fit residues: 41.2306 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 : 1.443 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.119770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.103772 restraints weight = 27609.304| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.12 r_work: 0.2890 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15013 Z= 0.138 Angle : 0.612 12.369 20743 Z= 0.241 Chirality : 0.035 0.132 2140 Planarity : 0.003 0.040 2491 Dihedral : 13.607 179.996 2705 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.89 % Allowed : 5.42 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.23), residues: 1341 helix: 4.24 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.40 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS G 36 PHE 0.008 0.001 PHE Z 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06311 ( 841) hydrogen bonds : angle 2.81521 ( 2322) covalent geometry : bond 0.00306 (14984) covalent geometry : angle 0.61177 (20743) Misc. bond : bond 0.00112 ( 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 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.270 Fit side-chains REVERT: A 37 MET cc_start: 0.8218 (mmt) cc_final: 0.7947 (mmt) REVERT: O 37 MET cc_start: 0.8107 (mmt) cc_final: 0.7902 (mmt) outliers start: 11 outliers final: 11 residues processed: 113 average time/residue: 0.2400 time to fit residues: 41.7736 Evaluate side-chains 117 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3931 r_free = 0.3931 target = 0.167254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159096 restraints weight = 25403.079| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 0.60 r_work: 0.3014 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1571 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= 0.131 Angle : 0.598 12.164 20743 Z= 0.236 Chirality : 0.035 0.127 2140 Planarity : 0.003 0.039 2491 Dihedral : 13.495 179.993 2705 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.97 % Allowed : 5.42 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.23), residues: 1341 helix: 4.30 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.42 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS G 36 PHE 0.008 0.001 PHE Z 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06093 ( 841) hydrogen bonds : angle 2.79269 ( 2322) covalent geometry : bond 0.00287 (14984) covalent geometry : angle 0.59850 (20743) Misc. bond : bond 0.00107 ( 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 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.212 Fit side-chains REVERT: 7 48 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: A 37 MET cc_start: 0.7841 (mmt) cc_final: 0.7517 (mmt) REVERT: K 37 MET cc_start: 0.7853 (mmt) cc_final: 0.7625 (mmt) REVERT: O 37 MET cc_start: 0.7791 (mmt) cc_final: 0.7497 (mmt) REVERT: W 37 MET cc_start: 0.7800 (mmt) cc_final: 0.7500 (mmt) outliers start: 12 outliers final: 11 residues processed: 112 average time/residue: 0.2291 time to fit residues: 39.6718 Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 K residue 53 VAL 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 104 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3196 r_free = 0.3196 target = 0.118267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101923 restraints weight = 30557.174| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.20 r_work: 0.2888 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15013 Z= 0.154 Angle : 0.650 12.381 20743 Z= 0.255 Chirality : 0.036 0.132 2140 Planarity : 0.003 0.039 2491 Dihedral : 13.711 179.980 2705 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.97 % Allowed : 5.42 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.49 (0.23), residues: 1341 helix: 4.19 (0.14), residues: 888 sheet: None (None), residues: 0 loop : 0.37 (0.34), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 12 HIS 0.003 0.001 HIS G 36 PHE 0.009 0.001 PHE T 21 TYR 0.007 0.001 TYR 7 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.06757 ( 841) hydrogen bonds : angle 2.85897 ( 2322) covalent geometry : bond 0.00354 (14984) covalent geometry : angle 0.65027 (20743) Misc. bond : bond 0.00130 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6900.66 seconds wall clock time: 120 minutes 3.00 seconds (7203.00 seconds total)