Starting phenix.real_space_refine on Thu Sep 18 01:28:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypb_39475/09_2025/8ypb_39475.cif" } resolution = 2.45 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= 0.074 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: 6 Type Number sf(0) Gaussians Ca 14 9.91 5 Mg 28 5.21 5 S 42 5.16 5 C 9422 2.51 5 N 1820 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 13286 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 49} 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: 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: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" 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: "D" 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: "E" 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: "G" 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: "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: 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: "J" 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: "K" 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: "L" 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: "M" 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: 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: "Q" 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: "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: 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" 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: "V" 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: "W" 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" 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: 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: "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} Time building chain proxies: 3.17, per 1000 atoms: 0.24 Number of scatterers: 13286 At special positions: 0 Unit cell: (117.52, 115.44, 71.76, 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 14 19.99 S 42 16.00 Mg 28 11.99 O 1960 8.00 N 1820 7.00 C 9422 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=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 541.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'b' and resid 11 through 44 Processing helix chain 'F' and resid 2 through 11 removed outlier: 4.509A pdb=" N TRP F 6 " --> pdb=" O PRO F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 39 Processing helix chain 'A' and resid 11 through 44 Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 13 through 39 Processing helix chain 'C' and resid 11 through 44 Processing helix chain 'D' and resid 2 through 11 removed outlier: 4.502A pdb=" N TRP D 6 " --> pdb=" O PRO D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 39 Processing helix chain 'E' and resid 11 through 44 Processing helix chain 'G' and resid 2 through 11 removed outlier: 4.404A pdb=" N TRP G 6 " --> pdb=" O PRO G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 39 Processing helix chain 'H' and resid 11 through 44 Processing helix chain 'I' and resid 4 through 11 Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 2 through 11 removed outlier: 4.421A pdb=" N TRP K 6 " --> pdb=" O PRO K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 39 Processing helix chain 'L' and resid 11 through 44 Processing helix chain 'M' and resid 4 through 11 Processing helix chain 'M' and resid 13 through 39 Processing helix chain 'N' and resid 11 through 44 Processing helix chain 'O' and resid 4 through 11 Processing helix chain 'O' and resid 13 through 39 Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 4 through 11 Processing helix chain 'Q' and resid 13 through 39 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 2 through 11 removed outlier: 4.412A pdb=" N TRP S 6 " --> pdb=" O PRO S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 39 Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 4 through 11 Processing helix chain 'U' and resid 13 through 39 Processing helix chain 'V' and resid 11 through 44 Processing helix chain 'W' and resid 4 through 11 Processing helix chain 'W' and resid 13 through 39 Processing helix chain 'X' and resid 11 through 44 Processing helix chain 'Y' and resid 4 through 11 Processing helix chain 'Y' and resid 13 through 39 Processing helix chain 'Z' and resid 11 through 44 Processing helix chain 'a' and resid 4 through 11 Processing helix chain 'a' and resid 13 through 39 817 hydrogen bonds defined for protein. 2226 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: 2.27 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3642 1.36 - 1.53: 9599 1.53 - 1.71: 381 1.71 - 1.89: 84 1.89 - 2.07: 112 Bond restraints: 13818 Sorted by residual: bond pdb=" CA ILE Y 49 " pdb=" C ILE Y 49 " ideal model delta sigma weight residual 1.522 1.570 -0.048 7.10e-03 1.98e+04 4.58e+01 bond pdb=" C TRP a 44 " pdb=" N LEU a 45 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.36e-02 5.41e+03 4.54e+01 bond pdb=" CA ILE M 49 " pdb=" C ILE M 49 " ideal model delta sigma weight residual 1.522 1.570 -0.048 7.10e-03 1.98e+04 4.53e+01 bond pdb=" CA ALA V 15 " pdb=" C ALA V 15 " ideal model delta sigma weight residual 1.522 1.434 0.087 1.40e-02 5.10e+03 3.88e+01 bond pdb=" C1A BCL V 101 " pdb=" CHA BCL V 101 " ideal model delta sigma weight residual 1.368 1.492 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 13813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16928 3.01 - 6.02: 1635 6.02 - 9.03: 441 9.03 - 12.04: 79 12.04 - 15.05: 125 Bond angle restraints: 19208 Sorted by residual: angle pdb=" N ALA I 52 " pdb=" CA ALA I 52 " pdb=" C ALA I 52 " ideal model delta sigma weight residual 110.33 124.23 -13.90 1.29e+00 6.01e-01 1.16e+02 angle pdb=" N ALA U 52 " pdb=" CA ALA U 52 " pdb=" C ALA U 52 " ideal model delta sigma weight residual 110.33 124.19 -13.86 1.29e+00 6.01e-01 1.15e+02 angle pdb=" N ALA D 52 " pdb=" CA ALA D 52 " pdb=" C ALA D 52 " ideal model delta sigma weight residual 110.43 123.81 -13.38 1.31e+00 5.83e-01 1.04e+02 angle pdb=" N ALA S 52 " pdb=" CA ALA S 52 " pdb=" C ALA S 52 " ideal model delta sigma weight residual 110.33 123.07 -12.74 1.29e+00 6.01e-01 9.75e+01 angle pdb=" N ALA W 52 " pdb=" CA ALA W 52 " pdb=" C ALA W 52 " ideal model delta sigma weight residual 110.43 123.28 -12.85 1.31e+00 5.83e-01 9.62e+01 ... (remaining 19203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 6809 36.00 - 72.00: 349 72.00 - 108.00: 24 108.00 - 143.99: 0 143.99 - 179.99: 14 Dihedral angle restraints: 7196 sinusoidal: 3374 harmonic: 3822 Sorted by residual: dihedral pdb=" C1 BCL K 101 " pdb=" C2 BCL K 101 " pdb=" C3 BCL K 101 " pdb=" C5 BCL K 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL Y 101 " pdb=" C2 BCL Y 101 " pdb=" C3 BCL Y 101 " pdb=" C5 BCL Y 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.01 179.99 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL S 101 " pdb=" C2 BCL S 101 " pdb=" C3 BCL S 101 " pdb=" C5 BCL S 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.05 179.95 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 1900 0.302 - 0.604: 31 0.604 - 0.906: 43 0.906 - 1.208: 0 1.208 - 1.510: 28 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C2C BCL a 102 " pdb=" C1C BCL a 102 " pdb=" C3C BCL a 102 " pdb=" CMC BCL a 102 " both_signs ideal model delta sigma weight residual False -2.62 -1.11 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C2C BCL F 101 " pdb=" C1C BCL F 101 " pdb=" C3C BCL F 101 " pdb=" CMC BCL F 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.11 -1.51 2.00e-01 2.50e+01 5.68e+01 chirality pdb=" C2C BCL O 101 " pdb=" C1C BCL O 101 " pdb=" C3C BCL O 101 " pdb=" CMC BCL O 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.12 -1.51 2.00e-01 2.50e+01 5.67e+01 ... (remaining 1999 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BCL U 101 " -0.236 2.20e-02 2.07e+03 2.07e-01 6.18e+02 pdb=" C1D BCL U 101 " -0.282 2.20e-02 2.07e+03 pdb=" C2D BCL U 101 " -0.077 2.20e-02 2.07e+03 pdb=" C3D BCL U 101 " 0.097 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 " 0.354 2.20e-02 2.07e+03 delta sigma weight rms_deltas residual plane pdb=" ND BCL I 101 " 0.236 2.20e-02 2.07e+03 2.06e-01 6.16e+02 pdb=" C1D BCL I 101 " 0.281 2.20e-02 2.07e+03 pdb=" C2D BCL I 101 " 0.077 2.20e-02 2.07e+03 pdb=" C3D BCL I 101 " -0.097 2.20e-02 2.07e+03 pdb=" C4D BCL I 101 " 0.008 2.20e-02 2.07e+03 pdb=" CHA BCL I 101 " -0.151 2.20e-02 2.07e+03 pdb=" CHD BCL I 101 " -0.354 2.20e-02 2.07e+03 delta sigma weight rms_deltas residual plane pdb=" ND BCL F 101 " -0.231 2.20e-02 2.07e+03 2.01e-01 5.86e+02 pdb=" C1D BCL F 101 " -0.275 2.20e-02 2.07e+03 pdb=" C2D BCL F 101 " -0.072 2.20e-02 2.07e+03 pdb=" C3D BCL F 101 " 0.095 2.20e-02 2.07e+03 pdb=" C4D BCL F 101 " -0.007 2.20e-02 2.07e+03 pdb=" CHA BCL F 101 " 0.147 2.20e-02 2.07e+03 pdb=" CHD BCL F 101 " 0.344 2.20e-02 2.07e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 73 2.44 - 3.06: 7605 3.06 - 3.67: 21240 3.67 - 4.29: 35724 4.29 - 4.90: 54331 Nonbonded interactions: 118973 Sorted by model distance: nonbonded pdb=" OD1 ASP I 47 " pdb="CA CA I 102 " model vdw 1.831 2.510 nonbonded pdb=" OD1 ASP a 47 " pdb="CA CA a 103 " model vdw 1.916 2.510 nonbonded pdb=" OD1 ASP F 47 " pdb="CA CA F 102 " model vdw 1.948 2.510 nonbonded pdb=" O ILE D 49 " pdb="CA CA D 102 " model vdw 1.950 2.510 nonbonded pdb=" OD1 ASP B 47 " pdb="CA CA B 102 " model vdw 1.953 2.510 ... (remaining 118968 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' selection = (chain 'C' and resid 6 through 101) selection = (chain 'E' and resid 6 through 101) selection = chain 'H' selection = (chain 'J' and resid 6 through 101) selection = (chain 'L' and resid 6 through 101) selection = (chain 'N' and resid 6 through 101) selection = (chain 'P' and resid 6 through 101) selection = chain 'R' selection = chain 'T' selection = (chain 'V' and resid 6 through 101) selection = chain 'X' selection = (chain 'Z' and resid 6 through 101) selection = chain 'b' } ncs_group { reference = (chain 'B' and resid 2 through 54) selection = (chain 'D' and resid 2 through 54) selection = (chain 'F' and resid 2 through 54) selection = (chain 'G' and resid 2 through 54) selection = (chain 'I' and resid 2 through 54) selection = (chain 'K' and resid 2 through 54) selection = (chain 'M' and resid 2 through 54) selection = (chain 'O' and resid 2 through 54) selection = (chain 'Q' and resid 2 through 54) selection = (chain 'S' and resid 2 through 54) selection = (chain 'U' and resid 2 through 54) selection = (chain 'W' and resid 2 through 54) selection = (chain 'Y' and resid 2 through 54) selection = (chain 'a' and resid 2 through 54) } 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: 4.040 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.143 13844 Z= 1.160 Angle : 2.225 15.054 19208 Z= 1.079 Chirality : 0.220 1.510 2002 Planarity : 0.027 0.207 2324 Dihedral : 20.953 179.992 4676 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.03 % Allowed : 15.43 % Favored : 82.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 25.00 % 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: 3.91 (0.22), residues: 1274 helix: 3.49 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 0.98 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 15 PHE 0.011 0.002 PHE O 42 TRP 0.029 0.001 TRP a 44 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.02210 (13818) covalent geometry : angle 2.22516 (19208) hydrogen bonds : bond 0.13564 ( 817) hydrogen bonds : angle 3.61156 ( 2226) Misc. bond : bond 0.11730 ( 26) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.486 Fit side-chains REVERT: B 53 LYS cc_start: 0.7165 (mptp) cc_final: 0.6165 (mttt) REVERT: G 53 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6288 (mttt) REVERT: I 53 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6062 (mttt) REVERT: S 53 LYS cc_start: 0.7306 (mptp) cc_final: 0.6419 (mttt) REVERT: U 15 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8417 (ttt-90) REVERT: U 53 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6063 (mttt) outliers start: 23 outliers final: 18 residues processed: 236 average time/residue: 0.6856 time to fit residues: 174.8206 Evaluate side-chains 218 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 49 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN H 24 GLN N 24 GLN T 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.164611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150559 restraints weight = 9736.579| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 0.42 r_work: 0.3448 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13844 Z= 0.142 Angle : 0.736 11.617 19208 Z= 0.282 Chirality : 0.040 0.142 2002 Planarity : 0.004 0.034 2324 Dihedral : 21.308 179.683 2303 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.41 % Allowed : 16.84 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.60 (0.22), residues: 1274 helix: 3.86 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.63 (0.33), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 PHE 0.015 0.002 PHE V 18 TRP 0.014 0.001 TRP a 44 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00326 (13818) covalent geometry : angle 0.73562 (19208) hydrogen bonds : bond 0.04627 ( 817) hydrogen bonds : angle 2.92307 ( 2226) Misc. bond : bond 0.00334 ( 26) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.446 Fit side-chains REVERT: G 4 ASP cc_start: 0.8038 (m-30) cc_final: 0.7788 (m-30) REVERT: J 17 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: P 7 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7362 (ptm) REVERT: R 17 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: S 4 ASP cc_start: 0.8031 (m-30) cc_final: 0.7799 (m-30) REVERT: V 16 GLN cc_start: 0.8600 (mt0) cc_final: 0.8159 (mt0) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.7544 time to fit residues: 179.8063 Evaluate side-chains 211 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN H 24 GLN N 24 GLN T 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147888 restraints weight = 9750.516| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 0.46 r_work: 0.3409 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13844 Z= 0.173 Angle : 0.798 11.423 19208 Z= 0.304 Chirality : 0.042 0.156 2002 Planarity : 0.004 0.034 2324 Dihedral : 21.951 179.638 2284 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.29 % Allowed : 16.58 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.47 (0.21), residues: 1274 helix: 3.77 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.55 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 16 PHE 0.016 0.003 PHE O 42 TRP 0.012 0.002 TRP Y 9 HIS 0.009 0.002 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00401 (13818) covalent geometry : angle 0.79829 (19208) hydrogen bonds : bond 0.04873 ( 817) hydrogen bonds : angle 3.03951 ( 2226) Misc. bond : bond 0.00422 ( 26) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.473 Fit side-chains REVERT: E 17 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: G 4 ASP cc_start: 0.8056 (m-30) cc_final: 0.7783 (m-30) REVERT: J 17 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: P 17 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: R 17 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: S 4 ASP cc_start: 0.8061 (m-30) cc_final: 0.7739 (m-30) REVERT: U 15 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8379 (ttt-90) REVERT: V 16 GLN cc_start: 0.8579 (mt0) cc_final: 0.8172 (mt0) outliers start: 26 outliers final: 10 residues processed: 208 average time/residue: 0.7861 time to fit residues: 175.2257 Evaluate side-chains 208 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.0010 chunk 99 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN X 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.164073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.149929 restraints weight = 9699.156| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 0.42 r_work: 0.3443 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13844 Z= 0.139 Angle : 0.749 10.648 19208 Z= 0.277 Chirality : 0.039 0.142 2002 Planarity : 0.004 0.032 2324 Dihedral : 21.757 179.707 2284 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.56 % Allowed : 17.11 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.66 (0.21), residues: 1274 helix: 3.91 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.64 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 PHE 0.013 0.002 PHE O 42 TRP 0.011 0.002 TRP Y 9 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00320 (13818) covalent geometry : angle 0.74896 (19208) hydrogen bonds : bond 0.04470 ( 817) hydrogen bonds : angle 2.90916 ( 2226) Misc. bond : bond 0.00323 ( 26) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.582 Fit side-chains REVERT: E 17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: I 34 MET cc_start: 0.8550 (mmt) cc_final: 0.8345 (mmt) REVERT: J 11 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8161 (p) REVERT: J 17 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: P 17 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: R 17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: V 17 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7675 (tt0) outliers start: 29 outliers final: 10 residues processed: 218 average time/residue: 0.7686 time to fit residues: 179.9057 Evaluate side-chains 211 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 17 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN H 24 GLN N 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.163866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.149575 restraints weight = 9735.782| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 0.42 r_work: 0.3437 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.004 0.027 13844 Z= 0.153 Angle : 0.777 9.965 19208 Z= 0.288 Chirality : 0.041 0.126 2002 Planarity : 0.004 0.033 2324 Dihedral : 21.859 179.642 2283 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 2.91 % Allowed : 16.67 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.60 (0.21), residues: 1274 helix: 3.83 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.68 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 PHE 0.014 0.002 PHE O 42 TRP 0.011 0.002 TRP Y 9 HIS 0.008 0.002 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00353 (13818) covalent geometry : angle 0.77691 (19208) hydrogen bonds : bond 0.04629 ( 817) hydrogen bonds : angle 2.95457 ( 2226) Misc. bond : bond 0.00370 ( 26) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.494 Fit side-chains REVERT: E 17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: J 11 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8153 (p) REVERT: J 17 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: P 17 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: Q 53 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5321 (mttt) REVERT: R 17 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: U 15 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8417 (ttt-90) REVERT: V 17 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7648 (tt0) outliers start: 33 outliers final: 18 residues processed: 213 average time/residue: 0.7834 time to fit residues: 179.0428 Evaluate side-chains 220 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.163944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.149658 restraints weight = 9689.235| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.42 r_work: 0.3442 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13844 Z= 0.147 Angle : 0.762 9.858 19208 Z= 0.281 Chirality : 0.040 0.116 2002 Planarity : 0.004 0.033 2324 Dihedral : 21.771 179.683 2283 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.26 % Allowed : 16.40 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.67 (0.21), residues: 1274 helix: 3.87 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.76 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 PHE 0.013 0.002 PHE O 42 TRP 0.011 0.002 TRP Y 9 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00337 (13818) covalent geometry : angle 0.76218 (19208) hydrogen bonds : bond 0.04530 ( 817) hydrogen bonds : angle 2.91700 ( 2226) Misc. bond : bond 0.00342 ( 26) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.549 Fit side-chains REVERT: E 17 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: J 11 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8148 (p) REVERT: J 17 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: P 7 MET cc_start: 0.7717 (ptm) cc_final: 0.7365 (ptm) REVERT: P 17 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: Q 53 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5225 (mttt) REVERT: R 17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: U 34 MET cc_start: 0.8534 (mmt) cc_final: 0.8302 (mmp) REVERT: V 17 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7546 (tt0) outliers start: 37 outliers final: 19 residues processed: 221 average time/residue: 0.7713 time to fit residues: 183.1890 Evaluate side-chains 220 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.164044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.149681 restraints weight = 9670.484| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 0.44 r_work: 0.3440 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13844 Z= 0.151 Angle : 0.774 9.851 19208 Z= 0.286 Chirality : 0.040 0.118 2002 Planarity : 0.004 0.033 2324 Dihedral : 21.760 179.681 2283 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.82 % Allowed : 16.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.65 (0.21), residues: 1274 helix: 3.83 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.81 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 PHE 0.013 0.002 PHE O 42 TRP 0.010 0.002 TRP Y 9 HIS 0.008 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00348 (13818) covalent geometry : angle 0.77443 (19208) hydrogen bonds : bond 0.04583 ( 817) hydrogen bonds : angle 2.93621 ( 2226) Misc. bond : bond 0.00354 ( 26) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.495 Fit side-chains REVERT: E 17 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: J 17 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: P 17 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: Q 53 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5327 (mttt) REVERT: R 17 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: U 15 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8392 (ttt-90) REVERT: V 17 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7560 (tt0) outliers start: 32 outliers final: 19 residues processed: 211 average time/residue: 0.7722 time to fit residues: 174.9619 Evaluate side-chains 218 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 66 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.166146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.152146 restraints weight = 9654.790| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 0.40 r_work: 0.3463 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13844 Z= 0.126 Angle : 0.727 9.098 19208 Z= 0.265 Chirality : 0.038 0.115 2002 Planarity : 0.003 0.031 2324 Dihedral : 21.482 179.775 2283 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 2.65 % Allowed : 17.02 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.86 (0.21), residues: 1274 helix: 3.99 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.88 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 16 PHE 0.011 0.002 PHE O 42 TRP 0.010 0.001 TRP M 9 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00287 (13818) covalent geometry : angle 0.72738 (19208) hydrogen bonds : bond 0.04290 ( 817) hydrogen bonds : angle 2.82346 ( 2226) Misc. bond : bond 0.00272 ( 26) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.597 Fit side-chains REVERT: E 17 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: J 17 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: P 7 MET cc_start: 0.7742 (ptm) cc_final: 0.7468 (ptp) REVERT: P 17 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: U 15 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8421 (ttt-90) REVERT: V 17 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7380 (tt0) outliers start: 30 outliers final: 16 residues processed: 215 average time/residue: 0.7726 time to fit residues: 178.2971 Evaluate side-chains 214 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN P 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.165320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.151139 restraints weight = 9732.307| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 0.42 r_work: 0.3449 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.142 Angle : 0.761 9.644 19208 Z= 0.281 Chirality : 0.039 0.118 2002 Planarity : 0.004 0.032 2324 Dihedral : 21.518 179.717 2283 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.94 % Allowed : 17.90 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.75 (0.21), residues: 1274 helix: 3.89 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.86 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 16 PHE 0.012 0.002 PHE O 42 TRP 0.010 0.002 TRP Y 9 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00323 (13818) covalent geometry : angle 0.76085 (19208) hydrogen bonds : bond 0.04474 ( 817) hydrogen bonds : angle 2.86467 ( 2226) Misc. bond : bond 0.00316 ( 26) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.498 Fit side-chains REVERT: E 17 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: J 17 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: P 17 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: R 17 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: U 15 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8413 (ttt-90) REVERT: V 17 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7449 (tt0) outliers start: 22 outliers final: 16 residues processed: 212 average time/residue: 0.7852 time to fit residues: 178.4304 Evaluate side-chains 214 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN P 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.166116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151562 restraints weight = 9691.808| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 0.40 r_work: 0.3465 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13844 Z= 0.134 Angle : 0.741 9.231 19208 Z= 0.273 Chirality : 0.039 0.116 2002 Planarity : 0.004 0.031 2324 Dihedral : 21.405 179.776 2283 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 2.29 % Allowed : 17.99 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.79 (0.21), residues: 1274 helix: 3.92 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.89 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 16 PHE 0.012 0.002 PHE O 42 TRP 0.010 0.001 TRP Y 9 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00305 (13818) covalent geometry : angle 0.74127 (19208) hydrogen bonds : bond 0.04375 ( 817) hydrogen bonds : angle 2.83131 ( 2226) Misc. bond : bond 0.00286 ( 26) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.482 Fit side-chains REVERT: E 17 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: J 17 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: N 7 MET cc_start: 0.7087 (ttt) cc_final: 0.6857 (ptm) REVERT: P 17 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: R 17 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: U 15 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8401 (ttt-90) REVERT: V 17 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7376 (tt0) outliers start: 26 outliers final: 17 residues processed: 209 average time/residue: 0.7751 time to fit residues: 173.8525 Evaluate side-chains 215 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 17 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.0020 chunk 99 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 GLN N 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.166331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153025 restraints weight = 9750.780| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 0.39 r_work: 0.3496 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13844 Z= 0.127 Angle : 0.725 9.094 19208 Z= 0.266 Chirality : 0.038 0.115 2002 Planarity : 0.003 0.031 2324 Dihedral : 21.279 179.794 2283 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 2.20 % Allowed : 17.72 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.84 (0.21), residues: 1274 helix: 3.96 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.92 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 16 PHE 0.010 0.002 PHE U 42 TRP 0.010 0.001 TRP Y 9 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00288 (13818) covalent geometry : angle 0.72525 (19208) hydrogen bonds : bond 0.04287 ( 817) hydrogen bonds : angle 2.79469 ( 2226) Misc. bond : bond 0.00266 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.10 seconds wall clock time: 91 minutes 48.35 seconds (5508.35 seconds total)