Starting phenix.real_space_refine on Wed Sep 17 22:56:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypd_39477/09_2025/8ypd_39477.cif" } resolution = 2.78 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 28 5.21 5 S 42 5.16 5 C 8820 2.51 5 N 1694 2.21 5 O 1708 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12292 Number of models: 1 Model: "" Number of chains: 56 Chain: "b" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "A" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "B" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "D" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "E" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "G" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "H" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "J" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "L" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "M" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "N" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "R" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "S" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "T" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "V" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "X" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Y" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "Z" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "a" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} 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: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "B" 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: "C" 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: 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: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" 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: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 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: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" 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: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "a" 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} Time building chain proxies: 2.60, per 1000 atoms: 0.21 Number of scatterers: 12292 At special positions: 0 Unit cell: (115.44, 113.36, 66.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 Mg 28 11.99 O 1708 8.00 N 1694 7.00 C 8820 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 412.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 80.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'b' and resid 11 through 44 removed outlier: 3.559A pdb=" N ILE b 21 " --> pdb=" O GLU b 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.538A pdb=" N ILE F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 35 Processing helix chain 'F' and resid 36 through 39 removed outlier: 3.679A pdb=" N ASN F 39 " --> pdb=" O PRO F 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 39' Processing helix chain 'A' and resid 11 through 44 removed outlier: 3.537A pdb=" N ILE A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 9 through 35 Processing helix chain 'C' and resid 11 through 44 removed outlier: 3.524A pdb=" N ILE C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 9 through 35 Processing helix chain 'D' and resid 36 through 39 removed outlier: 3.604A pdb=" N ASN D 39 " --> pdb=" O PRO D 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 39' Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.545A pdb=" N ILE E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 8 removed outlier: 3.514A pdb=" N ILE G 7 " --> pdb=" O LYS G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 34 Processing helix chain 'G' and resid 35 through 39 removed outlier: 3.720A pdb=" N ASN G 39 " --> pdb=" O PRO G 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 44 removed outlier: 3.516A pdb=" N ILE H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 9 through 35 Processing helix chain 'J' and resid 11 through 44 removed outlier: 3.661A pdb=" N ILE J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 11 through 35 Processing helix chain 'L' and resid 11 through 44 removed outlier: 3.571A pdb=" N ILE L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 7 Processing helix chain 'M' and resid 9 through 35 Processing helix chain 'N' and resid 11 through 44 removed outlier: 3.535A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 7 Processing helix chain 'O' and resid 9 through 35 Processing helix chain 'P' and resid 11 through 44 removed outlier: 3.576A pdb=" N ILE P 21 " --> pdb=" O GLU P 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 8 Processing helix chain 'Q' and resid 11 through 35 Processing helix chain 'R' and resid 11 through 44 removed outlier: 3.539A pdb=" N ILE R 21 " --> pdb=" O GLU R 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 7 Processing helix chain 'S' and resid 9 through 35 Processing helix chain 'S' and resid 36 through 39 removed outlier: 3.608A pdb=" N ASN S 39 " --> pdb=" O PRO S 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 36 through 39' Processing helix chain 'T' and resid 11 through 44 removed outlier: 3.543A pdb=" N ILE T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 11 through 35 Processing helix chain 'U' and resid 36 through 39 removed outlier: 3.639A pdb=" N ASN U 39 " --> pdb=" O PRO U 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 36 through 39' Processing helix chain 'V' and resid 11 through 44 removed outlier: 3.513A pdb=" N ILE V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 8 Processing helix chain 'W' and resid 9 through 35 Processing helix chain 'X' and resid 11 through 44 removed outlier: 3.557A pdb=" N ILE X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 7 Processing helix chain 'Y' and resid 9 through 35 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.729A pdb=" N ILE Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 9 through 35 Processing helix chain 'a' and resid 36 through 39 removed outlier: 3.680A pdb=" N ASN a 39 " --> pdb=" O PRO a 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 36 through 39' 756 hydrogen bonds defined for protein. 2217 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: 1.78 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.33: 2167 1.33 - 1.52: 6832 1.52 - 1.70: 3657 1.70 - 1.89: 84 1.89 - 2.07: 112 Bond restraints: 12852 Sorted by residual: bond pdb=" CA THR U 13 " pdb=" C THR U 13 " ideal model delta sigma weight residual 1.524 1.379 0.144 1.37e-02 5.33e+03 1.11e+02 bond pdb=" CA ASP B 9 " pdb=" C ASP B 9 " ideal model delta sigma weight residual 1.528 1.422 0.106 1.08e-02 8.57e+03 9.57e+01 bond pdb=" CA THR a 13 " pdb=" C THR a 13 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.32e-02 5.74e+03 9.11e+01 bond pdb=" CA THR M 13 " pdb=" C THR M 13 " ideal model delta sigma weight residual 1.524 1.399 0.125 1.32e-02 5.74e+03 8.99e+01 bond pdb=" CA THR W 13 " pdb=" C THR W 13 " ideal model delta sigma weight residual 1.524 1.400 0.124 1.32e-02 5.74e+03 8.81e+01 ... (remaining 12847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 15711 3.03 - 6.07: 1528 6.07 - 9.10: 390 9.10 - 12.13: 67 12.13 - 15.17: 126 Bond angle restraints: 17822 Sorted by residual: angle pdb=" C1D BCL T 101 " pdb=" CHD BCL T 101 " pdb=" C4C BCL T 101 " ideal model delta sigma weight residual 128.34 113.85 14.49 2.01e+00 2.49e-01 5.22e+01 angle pdb=" C1D BCL H 101 " pdb=" CHD BCL H 101 " pdb=" C4C BCL H 101 " ideal model delta sigma weight residual 128.34 113.91 14.43 2.01e+00 2.49e-01 5.18e+01 angle pdb=" C1D BCL V 101 " pdb=" CHD BCL V 101 " pdb=" C4C BCL V 101 " ideal model delta sigma weight residual 128.34 113.96 14.38 2.01e+00 2.49e-01 5.14e+01 angle pdb=" C1D BCL C 101 " pdb=" CHD BCL C 101 " pdb=" C4C BCL C 101 " ideal model delta sigma weight residual 128.34 113.97 14.37 2.01e+00 2.49e-01 5.13e+01 angle pdb=" C1D BCL R 101 " pdb=" CHD BCL R 101 " pdb=" C4C BCL R 101 " ideal model delta sigma weight residual 128.34 114.00 14.34 2.01e+00 2.49e-01 5.11e+01 ... (remaining 17817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 6254 35.98 - 71.96: 209 71.96 - 107.95: 19 107.95 - 143.93: 0 143.93 - 179.91: 14 Dihedral angle restraints: 6496 sinusoidal: 3122 harmonic: 3374 Sorted by residual: dihedral pdb=" C1 BCL F 101 " pdb=" C2 BCL F 101 " pdb=" C3 BCL F 101 " pdb=" C5 BCL F 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.09 -179.91 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL I 101 " pdb=" C2 BCL I 101 " pdb=" C3 BCL I 101 " pdb=" C5 BCL I 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.10 -179.90 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL O 101 " pdb=" C2 BCL O 101 " pdb=" C3 BCL O 101 " pdb=" C5 BCL O 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.12 -179.88 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 6493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1660 0.299 - 0.598: 21 0.598 - 0.897: 41 0.897 - 1.196: 0 1.196 - 1.495: 28 Chirality restraints: 1750 Sorted by residual: chirality pdb=" C2C BCL K 101 " pdb=" C1C BCL K 101 " pdb=" C3C BCL K 101 " pdb=" CMC BCL K 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.13 -1.50 2.00e-01 2.50e+01 5.59e+01 chirality pdb=" C2C BCL Y 101 " pdb=" C1C BCL Y 101 " pdb=" C3C BCL Y 101 " pdb=" CMC BCL Y 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.13 -1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" C2C BCL C 101 " pdb=" C1C BCL C 101 " pdb=" C3C BCL C 101 " pdb=" CMC BCL C 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.13 -1.49 2.00e-01 2.50e+01 5.54e+01 ... (remaining 1747 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BCL O 101 " 0.237 2.20e-02 2.07e+03 2.09e-01 6.33e+02 pdb=" C1D BCL O 101 " 0.287 2.20e-02 2.07e+03 pdb=" C2D BCL O 101 " 0.078 2.20e-02 2.07e+03 pdb=" C3D BCL O 101 " -0.098 2.20e-02 2.07e+03 pdb=" C4D BCL O 101 " 0.006 2.20e-02 2.07e+03 pdb=" CHA BCL O 101 " -0.152 2.20e-02 2.07e+03 pdb=" CHD BCL O 101 " -0.359 2.20e-02 2.07e+03 delta sigma weight rms_deltas residual plane pdb=" ND BCL U 101 " -0.236 2.20e-02 2.07e+03 2.08e-01 6.27e+02 pdb=" C1D BCL U 101 " -0.285 2.20e-02 2.07e+03 pdb=" C2D BCL U 101 " -0.078 2.20e-02 2.07e+03 pdb=" C3D BCL U 101 " 0.099 2.20e-02 2.07e+03 pdb=" C4D BCL U 101 " -0.008 2.20e-02 2.07e+03 pdb=" CHA BCL U 101 " 0.152 2.20e-02 2.07e+03 pdb=" CHD BCL U 101 " 0.357 2.20e-02 2.07e+03 delta sigma weight rms_deltas residual plane pdb=" ND BCL G 101 " 0.234 2.20e-02 2.07e+03 2.07e-01 6.17e+02 pdb=" C1D BCL G 101 " 0.283 2.20e-02 2.07e+03 pdb=" C2D BCL G 101 " 0.077 2.20e-02 2.07e+03 pdb=" C3D BCL G 101 " -0.098 2.20e-02 2.07e+03 pdb=" C4D BCL G 101 " 0.008 2.20e-02 2.07e+03 pdb=" CHA BCL G 101 " -0.150 2.20e-02 2.07e+03 pdb=" CHD BCL G 101 " -0.354 2.20e-02 2.07e+03 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 4090 2.92 - 3.41: 11604 3.41 - 3.91: 23893 3.91 - 4.40: 26525 4.40 - 4.90: 42917 Nonbonded interactions: 109029 Sorted by model distance: nonbonded pdb=" O LEU D 41 " pdb=" OG SER G 35 " model vdw 2.421 3.040 nonbonded pdb=" O ASP G 9 " pdb=" OG1 THR G 13 " model vdw 2.446 3.040 nonbonded pdb=" N THR U 13 " pdb=" N LEU U 14 " model vdw 2.458 2.560 nonbonded pdb=" OE1 GLU J 12 " pdb=" CE LYS K 3 " model vdw 2.460 3.440 nonbonded pdb=" O VAL P 23 " pdb=" OG1 THR P 27 " model vdw 2.467 3.040 ... (remaining 109024 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 'A' and resid 6 through 101) selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = (chain 'B' and resid 1 through 43) selection = (chain 'D' and resid 1 through 43) selection = (chain 'F' and resid 1 through 43) selection = (chain 'G' and resid 1 through 43) selection = (chain 'I' and resid 1 through 43) selection = (chain 'K' and resid 1 through 43) selection = (chain 'M' and resid 1 through 43) selection = (chain 'O' and resid 1 through 43) selection = (chain 'Q' and resid 1 through 43) selection = (chain 'S' and resid 1 through 43) selection = (chain 'U' and resid 1 through 43) selection = (chain 'W' and resid 1 through 43) selection = (chain 'Y' and resid 1 through 43) selection = (chain 'a' and resid 1 through 43) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.360 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.023 0.144 12880 Z= 1.205 Angle : 2.271 15.168 17822 Z= 1.065 Chirality : 0.230 1.495 1750 Planarity : 0.028 0.209 2170 Dihedral : 19.277 179.909 4284 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.49 % Allowed : 0.88 % Favored : 98.63 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1134 helix: 0.52 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 1.21 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 11 PHE 0.012 0.001 PHE a 20 TRP 0.020 0.002 TRP Q 5 HIS 0.004 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.02284 (12852) covalent geometry : angle 2.27132 (17822) hydrogen bonds : bond 0.13102 ( 756) hydrogen bonds : angle 6.01359 ( 2217) Misc. bond : bond 0.11860 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.333 Fit side-chains REVERT: C 27 THR cc_start: 0.9063 (m) cc_final: 0.8861 (m) REVERT: I 1 MET cc_start: 0.7912 (tpt) cc_final: 0.7320 (tpt) REVERT: J 16 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7461 (mm-40) REVERT: O 3 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8064 (mtpm) REVERT: R 27 THR cc_start: 0.9068 (m) cc_final: 0.8867 (m) REVERT: T 17 GLU cc_start: 0.7407 (tt0) cc_final: 0.7080 (tm-30) REVERT: V 12 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (mt-10) outliers start: 5 outliers final: 1 residues processed: 93 average time/residue: 0.6586 time to fit residues: 66.2130 Evaluate side-chains 89 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain U residue 10 PRO Chi-restraints excluded: chain V residue 12 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107518 restraints weight = 11580.190| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 0.71 r_work: 0.2960 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12880 Z= 0.156 Angle : 0.746 7.915 17822 Z= 0.279 Chirality : 0.039 0.147 1750 Planarity : 0.005 0.068 2170 Dihedral : 22.818 179.614 2151 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.24), residues: 1134 helix: 1.68 (0.16), residues: 868 sheet: None (None), residues: 0 loop : -0.19 (0.46), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 44 PHE 0.011 0.001 PHE a 20 TRP 0.011 0.002 TRP W 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00381 (12852) covalent geometry : angle 0.74556 (17822) hydrogen bonds : bond 0.03825 ( 756) hydrogen bonds : angle 3.71763 ( 2217) Misc. bond : bond 0.00321 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.435 Fit side-chains REVERT: C 27 THR cc_start: 0.9013 (m) cc_final: 0.8807 (m) REVERT: J 17 GLU cc_start: 0.8064 (tt0) cc_final: 0.7719 (tm-30) REVERT: L 17 GLU cc_start: 0.7960 (tt0) cc_final: 0.7625 (tm-30) REVERT: R 27 THR cc_start: 0.9013 (m) cc_final: 0.8805 (m) REVERT: V 12 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7624 (tt0) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.5862 time to fit residues: 63.9799 Evaluate side-chains 98 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 12 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 82 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108420 restraints weight = 11569.288| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.72 r_work: 0.2970 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12880 Z= 0.136 Angle : 0.694 7.957 17822 Z= 0.256 Chirality : 0.037 0.139 1750 Planarity : 0.004 0.057 2170 Dihedral : 22.651 179.571 2145 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 5.77 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.24), residues: 1134 helix: 2.20 (0.15), residues: 868 sheet: None (None), residues: 0 loop : -0.15 (0.45), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 11 PHE 0.009 0.001 PHE G 38 TRP 0.009 0.001 TRP D 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00331 (12852) covalent geometry : angle 0.69433 (17822) hydrogen bonds : bond 0.03608 ( 756) hydrogen bonds : angle 3.40463 ( 2217) Misc. bond : bond 0.00267 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.419 Fit side-chains REVERT: F 11 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7920 (ttp-170) REVERT: C 27 THR cc_start: 0.9020 (m) cc_final: 0.8810 (m) REVERT: L 17 GLU cc_start: 0.7973 (tt0) cc_final: 0.7630 (tm-30) REVERT: R 27 THR cc_start: 0.9014 (m) cc_final: 0.8798 (m) outliers start: 6 outliers final: 0 residues processed: 108 average time/residue: 0.5475 time to fit residues: 64.7435 Evaluate side-chains 103 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN W 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105837 restraints weight = 11484.444| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.71 r_work: 0.2939 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 12880 Z= 0.198 Angle : 0.819 9.313 17822 Z= 0.300 Chirality : 0.042 0.151 1750 Planarity : 0.005 0.039 2170 Dihedral : 23.036 179.342 2142 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.49 % Allowed : 7.05 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.24), residues: 1134 helix: 2.19 (0.15), residues: 854 sheet: None (None), residues: 0 loop : 0.52 (0.46), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 44 PHE 0.012 0.002 PHE G 38 TRP 0.011 0.002 TRP D 5 HIS 0.007 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00494 (12852) covalent geometry : angle 0.81879 (17822) hydrogen bonds : bond 0.03878 ( 756) hydrogen bonds : angle 3.53695 ( 2217) Misc. bond : bond 0.00379 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.434 Fit side-chains REVERT: F 3 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7798 (mtpm) REVERT: F 11 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7861 (ttp-170) REVERT: C 27 THR cc_start: 0.9064 (m) cc_final: 0.8839 (m) REVERT: Y 3 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8217 (mtpm) outliers start: 5 outliers final: 0 residues processed: 100 average time/residue: 0.6057 time to fit residues: 65.6655 Evaluate side-chains 96 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109222 restraints weight = 11568.703| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.69 r_work: 0.2967 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12880 Z= 0.145 Angle : 0.717 8.177 17822 Z= 0.261 Chirality : 0.038 0.142 1750 Planarity : 0.004 0.039 2170 Dihedral : 22.603 179.465 2142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.20 % Allowed : 7.73 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.22), residues: 1134 helix: 3.32 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.67 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 44 PHE 0.010 0.001 PHE D 38 TRP 0.010 0.002 TRP D 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00355 (12852) covalent geometry : angle 0.71739 (17822) hydrogen bonds : bond 0.03626 ( 756) hydrogen bonds : angle 3.35389 ( 2217) Misc. bond : bond 0.00278 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.384 Fit side-chains REVERT: F 11 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7998 (ttp-170) REVERT: A 7 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.5384 (ptp) REVERT: C 27 THR cc_start: 0.9091 (m) cc_final: 0.8889 (m) REVERT: R 27 THR cc_start: 0.9096 (m) cc_final: 0.8887 (m) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.5635 time to fit residues: 66.0420 Evaluate side-chains 105 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain A residue 7 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110460 restraints weight = 11403.279| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.65 r_work: 0.2985 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12880 Z= 0.132 Angle : 0.688 7.825 17822 Z= 0.249 Chirality : 0.037 0.137 1750 Planarity : 0.004 0.038 2170 Dihedral : 22.342 179.455 2142 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.49 % Allowed : 7.63 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.97 (0.22), residues: 1134 helix: 3.50 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.68 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 11 PHE 0.009 0.001 PHE K 38 TRP 0.009 0.001 TRP D 5 HIS 0.004 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00318 (12852) covalent geometry : angle 0.68756 (17822) hydrogen bonds : bond 0.03556 ( 756) hydrogen bonds : angle 3.24547 ( 2217) Misc. bond : bond 0.00256 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.425 Fit side-chains REVERT: F 11 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7984 (ttp-170) REVERT: A 7 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.5055 (ptp) REVERT: C 27 THR cc_start: 0.9083 (m) cc_final: 0.8881 (m) REVERT: L 17 GLU cc_start: 0.7990 (tt0) cc_final: 0.7712 (tm-30) REVERT: M 14 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8277 (mp) REVERT: R 27 THR cc_start: 0.9056 (m) cc_final: 0.8841 (m) outliers start: 5 outliers final: 0 residues processed: 113 average time/residue: 0.5265 time to fit residues: 65.3868 Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain M residue 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106900 restraints weight = 11416.067| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 0.71 r_work: 0.2954 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 12880 Z= 0.164 Angle : 0.756 8.238 17822 Z= 0.275 Chirality : 0.039 0.145 1750 Planarity : 0.004 0.039 2170 Dihedral : 22.640 179.390 2142 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 7.73 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.81 (0.22), residues: 1134 helix: 3.40 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.57 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 44 PHE 0.010 0.001 PHE G 38 TRP 0.010 0.002 TRP D 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00403 (12852) covalent geometry : angle 0.75602 (17822) hydrogen bonds : bond 0.03725 ( 756) hydrogen bonds : angle 3.35179 ( 2217) Misc. bond : bond 0.00325 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.422 Fit side-chains REVERT: F 11 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7854 (ttp-170) REVERT: A 7 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4955 (ptp) REVERT: C 27 THR cc_start: 0.9049 (m) cc_final: 0.8833 (m) REVERT: I 14 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8168 (mp) REVERT: L 17 GLU cc_start: 0.7882 (tt0) cc_final: 0.7546 (tm-30) REVERT: M 14 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8128 (mp) REVERT: a 14 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8067 (mp) outliers start: 6 outliers final: 0 residues processed: 107 average time/residue: 0.5607 time to fit residues: 65.5643 Evaluate side-chains 106 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain a residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107538 restraints weight = 11460.379| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 0.71 r_work: 0.2962 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12880 Z= 0.147 Angle : 0.723 8.060 17822 Z= 0.261 Chirality : 0.038 0.140 1750 Planarity : 0.004 0.039 2170 Dihedral : 22.448 179.432 2142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.68 % Allowed : 7.63 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (0.22), residues: 1134 helix: 3.51 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.59 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 44 PHE 0.010 0.001 PHE D 38 TRP 0.009 0.002 TRP S 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00358 (12852) covalent geometry : angle 0.72290 (17822) hydrogen bonds : bond 0.03642 ( 756) hydrogen bonds : angle 3.29444 ( 2217) Misc. bond : bond 0.00287 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.349 Fit side-chains REVERT: F 11 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7877 (ttp-170) REVERT: B 14 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8056 (mp) REVERT: C 27 THR cc_start: 0.9048 (m) cc_final: 0.8836 (m) REVERT: L 17 GLU cc_start: 0.7867 (tt0) cc_final: 0.7539 (tm-30) REVERT: M 14 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8161 (mp) REVERT: R 27 THR cc_start: 0.9042 (m) cc_final: 0.8823 (m) REVERT: a 14 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8063 (mp) outliers start: 7 outliers final: 1 residues processed: 110 average time/residue: 0.5196 time to fit residues: 62.7094 Evaluate side-chains 108 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain a residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107513 restraints weight = 11374.707| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 0.71 r_work: 0.2957 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 12880 Z= 0.147 Angle : 0.729 8.023 17822 Z= 0.264 Chirality : 0.038 0.140 1750 Planarity : 0.004 0.039 2170 Dihedral : 22.469 179.427 2142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 0.68 % Allowed : 7.73 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.22), residues: 1134 helix: 3.50 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.56 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 44 PHE 0.012 0.001 PHE a 20 TRP 0.009 0.002 TRP S 5 HIS 0.005 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00359 (12852) covalent geometry : angle 0.72895 (17822) hydrogen bonds : bond 0.03661 ( 756) hydrogen bonds : angle 3.29221 ( 2217) Misc. bond : bond 0.00293 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.470 Fit side-chains REVERT: F 11 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (ttp-170) REVERT: B 14 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mp) REVERT: C 27 THR cc_start: 0.9051 (m) cc_final: 0.8837 (m) REVERT: M 14 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8163 (mp) REVERT: R 27 THR cc_start: 0.9046 (m) cc_final: 0.8826 (m) REVERT: a 14 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8065 (mp) outliers start: 7 outliers final: 2 residues processed: 109 average time/residue: 0.5471 time to fit residues: 65.1534 Evaluate side-chains 110 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain a residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 104 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110598 restraints weight = 11486.907| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 0.65 r_work: 0.2987 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12880 Z= 0.128 Angle : 0.684 7.725 17822 Z= 0.247 Chirality : 0.037 0.137 1750 Planarity : 0.004 0.039 2170 Dihedral : 22.227 179.468 2142 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 7.93 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.09 (0.22), residues: 1134 helix: 3.63 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.61 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 44 PHE 0.009 0.001 PHE D 38 TRP 0.009 0.001 TRP D 5 HIS 0.004 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00308 (12852) covalent geometry : angle 0.68364 (17822) hydrogen bonds : bond 0.03565 ( 756) hydrogen bonds : angle 3.20885 ( 2217) Misc. bond : bond 0.00247 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.372 Fit side-chains REVERT: C 27 THR cc_start: 0.9086 (m) cc_final: 0.8883 (m) REVERT: R 27 THR cc_start: 0.9058 (m) cc_final: 0.8844 (m) REVERT: a 14 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8234 (mp) outliers start: 6 outliers final: 0 residues processed: 114 average time/residue: 0.5296 time to fit residues: 66.2015 Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107752 restraints weight = 11425.916| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 0.72 r_work: 0.2977 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12880 Z= 0.139 Angle : 0.711 8.036 17822 Z= 0.258 Chirality : 0.038 0.140 1750 Planarity : 0.004 0.041 2170 Dihedral : 22.355 179.435 2142 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.39 % Allowed : 8.12 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.05 (0.22), residues: 1134 helix: 3.61 (0.13), residues: 770 sheet: None (None), residues: 0 loop : 0.57 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 44 PHE 0.015 0.001 PHE a 20 TRP 0.010 0.002 TRP S 5 HIS 0.004 0.001 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00336 (12852) covalent geometry : angle 0.71121 (17822) hydrogen bonds : bond 0.03628 ( 756) hydrogen bonds : angle 3.24988 ( 2217) Misc. bond : bond 0.00278 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.34 seconds wall clock time: 59 minutes 22.16 seconds (3562.16 seconds total)