Starting phenix.real_space_refine on Thu May 15 09:00:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypb_39475/05_2025/8ypb_39475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypb_39475/05_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_39475/05_2025/8ypb_39475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypb_39475/05_2025/8ypb_39475.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypb_39475/05_2025/8ypb_39475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypb_39475/05_2025/8ypb_39475.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.70, per 1000 atoms: 0.65 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: 4.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.96 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: 3.79 Time building geometry restraints manager: 4.80 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 47 or resid 101)) selection = (chain 'E' and (resid 6 through 47 or resid 101)) selection = chain 'H' selection = (chain 'J' and (resid 6 through 47 or resid 101)) selection = (chain 'L' and (resid 6 through 47 or resid 101)) selection = (chain 'N' and (resid 6 through 47 or resid 101)) selection = (chain 'P' and (resid 6 through 47 or resid 101)) selection = chain 'R' selection = chain 'T' selection = (chain 'V' and (resid 6 through 47 or resid 101)) selection = chain 'X' selection = (chain 'Z' and (resid 6 through 47 or resid 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: 2.280 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.060 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- 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 : 14.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (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 TRP 0.029 0.001 TRP a 44 HIS 0.005 0.001 HIS C 37 PHE 0.011 0.002 PHE O 42 ARG 0.009 0.001 ARG M 15 Details of bonding type rmsd hydrogen bonds : bond 0.13564 ( 817) hydrogen bonds : angle 3.61156 ( 2226) covalent geometry : bond 0.02210 (13818) covalent geometry : angle 2.22516 (19208) 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 : 1.266 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: 1.3450 time to fit residues: 343.3696 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 : 1.312 ------------------------------------------------------------------------------- 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 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.164505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150641 restraints weight = 9659.473| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.41 r_work: 0.3446 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1036 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 : 0.732 11.528 19208 Z= 0.282 Chirality : 0.039 0.140 2002 Planarity : 0.004 0.034 2324 Dihedral : 21.300 179.687 2303 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.22), residues: 1274 helix: 3.85 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.64 (0.33), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 44 HIS 0.007 0.001 HIS A 37 PHE 0.014 0.002 PHE V 18 ARG 0.003 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 817) hydrogen bonds : angle 2.93204 ( 2226) covalent geometry : bond 0.00327 (13818) covalent geometry : angle 0.73239 (19208) Misc. bond : bond 0.00336 ( 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 : 1.205 Fit side-chains REVERT: G 4 ASP cc_start: 0.8035 (m-30) cc_final: 0.7789 (m-30) REVERT: J 17 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: M 4 ASP cc_start: 0.8071 (m-30) cc_final: 0.7851 (m-30) REVERT: P 7 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7366 (ptm) REVERT: R 17 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: S 4 ASP cc_start: 0.8027 (m-30) cc_final: 0.7796 (m-30) REVERT: V 16 GLN cc_start: 0.8601 (mt0) cc_final: 0.8153 (mt0) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 1.4758 time to fit residues: 352.4752 Evaluate side-chains 210 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.164010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.149836 restraints weight = 9664.835| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 0.42 r_work: 0.3441 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1286 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= 0.144 Angle : 0.749 10.316 19208 Z= 0.282 Chirality : 0.040 0.153 2002 Planarity : 0.004 0.032 2324 Dihedral : 21.750 179.667 2284 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.38 % Allowed : 16.84 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.21), residues: 1274 helix: 3.91 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.60 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 9 HIS 0.008 0.001 HIS A 37 PHE 0.013 0.002 PHE U 42 ARG 0.004 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 817) hydrogen bonds : angle 2.92934 ( 2226) covalent geometry : bond 0.00329 (13818) covalent geometry : angle 0.74943 (19208) Misc. bond : bond 0.00343 ( 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 227 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.404 Fit side-chains REVERT: E 17 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: J 17 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: P 17 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: R 17 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: U 15 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8388 (ttt-90) REVERT: V 16 GLN cc_start: 0.8560 (mt0) cc_final: 0.8298 (mt0) REVERT: V 17 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: W 53 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5883 (mttt) outliers start: 27 outliers final: 8 residues processed: 210 average time/residue: 1.5177 time to fit residues: 342.3000 Evaluate side-chains 207 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 W residue 53 LYS Chi-restraints excluded: chain Z residue 17 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 P 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.166901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153186 restraints weight = 9613.151| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.40 r_work: 0.3466 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1338 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= 0.119 Angle : 0.710 9.798 19208 Z= 0.257 Chirality : 0.037 0.135 2002 Planarity : 0.003 0.029 2324 Dihedral : 21.464 179.785 2283 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.82 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.21), residues: 1274 helix: 4.09 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.69 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 9 HIS 0.006 0.001 HIS A 37 PHE 0.011 0.002 PHE O 42 ARG 0.004 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 817) hydrogen bonds : angle 2.79000 ( 2226) covalent geometry : bond 0.00270 (13818) covalent geometry : angle 0.71043 (19208) Misc. bond : bond 0.00248 ( 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 236 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.331 Fit side-chains REVERT: E 17 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: J 17 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: P 17 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: V 17 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: W 53 LYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5911 (mttt) outliers start: 32 outliers final: 10 residues processed: 216 average time/residue: 1.5520 time to fit residues: 359.4186 Evaluate side-chains 210 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain D residue 54 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 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 V residue 17 GLU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.163424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149125 restraints weight = 9703.455| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 0.43 r_work: 0.3435 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13844 Z= 0.175 Angle : 0.811 10.497 19208 Z= 0.303 Chirality : 0.043 0.137 2002 Planarity : 0.004 0.034 2324 Dihedral : 21.903 179.628 2283 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.65 % Allowed : 17.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.21), residues: 1274 helix: 3.81 (0.14), residues: 812 sheet: None (None), residues: 0 loop : 1.69 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 9 HIS 0.009 0.002 HIS b 37 PHE 0.016 0.003 PHE O 42 ARG 0.004 0.001 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 817) hydrogen bonds : angle 2.99800 ( 2226) covalent geometry : bond 0.00404 (13818) covalent geometry : angle 0.81055 (19208) Misc. bond : bond 0.00428 ( 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: 30 poor density : 199 time to evaluate : 1.391 Fit side-chains REVERT: E 17 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: J 17 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: P 17 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: R 17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: V 17 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7575 (tm-30) outliers start: 30 outliers final: 17 residues processed: 214 average time/residue: 1.5230 time to fit residues: 349.9659 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 : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 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 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.166478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152665 restraints weight = 9796.275| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 0.41 r_work: 0.3464 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1419 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= 0.121 Angle : 0.713 9.011 19208 Z= 0.259 Chirality : 0.038 0.117 2002 Planarity : 0.003 0.031 2324 Dihedral : 21.426 179.808 2283 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.21), residues: 1274 helix: 4.02 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.79 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 9 HIS 0.005 0.001 HIS A 37 PHE 0.011 0.002 PHE O 42 ARG 0.004 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 817) hydrogen bonds : angle 2.81027 ( 2226) covalent geometry : bond 0.00274 (13818) covalent geometry : angle 0.71283 (19208) Misc. bond : bond 0.00256 ( 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 230 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.303 Fit side-chains REVERT: E 17 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: J 17 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: P 17 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: R 17 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: V 17 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7421 (tm-30) outliers start: 29 outliers final: 16 residues processed: 215 average time/residue: 1.4336 time to fit residues: 331.6558 Evaluate side-chains 215 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.0470 chunk 102 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.166849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152241 restraints weight = 9708.701| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.41 r_work: 0.3468 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1432 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= 0.121 Angle : 0.715 9.045 19208 Z= 0.259 Chirality : 0.038 0.114 2002 Planarity : 0.003 0.030 2324 Dihedral : 21.330 179.787 2283 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.65 % Allowed : 17.46 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.21), residues: 1274 helix: 4.04 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.84 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 9 HIS 0.005 0.001 HIS A 37 PHE 0.010 0.002 PHE O 42 ARG 0.005 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 817) hydrogen bonds : angle 2.78342 ( 2226) covalent geometry : bond 0.00274 (13818) covalent geometry : angle 0.71495 (19208) Misc. bond : bond 0.00258 ( 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 231 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.231 Fit side-chains REVERT: E 17 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: J 17 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: N 7 MET cc_start: 0.6981 (ttt) cc_final: 0.6638 (ptm) REVERT: P 17 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: R 17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: V 17 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7409 (tm-30) outliers start: 30 outliers final: 15 residues processed: 217 average time/residue: 1.4175 time to fit residues: 330.5560 Evaluate side-chains 212 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3752 r_free = 0.3752 target = 0.164749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.150478 restraints weight = 9751.594| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 0.43 r_work: 0.3442 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.030 13844 Z= 0.144 Angle : 0.757 9.695 19208 Z= 0.279 Chirality : 0.040 0.118 2002 Planarity : 0.004 0.031 2324 Dihedral : 21.448 179.718 2283 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.73 % Allowed : 17.64 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.75 (0.21), residues: 1274 helix: 3.91 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.84 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Y 9 HIS 0.007 0.001 HIS A 37 PHE 0.012 0.002 PHE O 42 ARG 0.005 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 817) hydrogen bonds : angle 2.86267 ( 2226) covalent geometry : bond 0.00328 (13818) covalent geometry : angle 0.75672 (19208) Misc. bond : bond 0.00333 ( 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 223 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.241 Fit side-chains REVERT: C 17 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: E 17 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: J 17 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: P 17 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: Q 53 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5450 (mttt) REVERT: R 17 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: V 17 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7412 (tm-30) outliers start: 31 outliers final: 16 residues processed: 208 average time/residue: 1.4472 time to fit residues: 323.9199 Evaluate side-chains 211 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 17 GLU 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 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 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.151963 restraints weight = 9682.097| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.42 r_work: 0.3459 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1468 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= 0.128 Angle : 0.725 9.038 19208 Z= 0.266 Chirality : 0.038 0.114 2002 Planarity : 0.003 0.030 2324 Dihedral : 21.303 179.799 2283 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.56 % Allowed : 17.64 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.21), residues: 1274 helix: 3.98 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.87 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 9 HIS 0.006 0.001 HIS A 37 PHE 0.011 0.002 PHE I 42 ARG 0.005 0.000 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 817) hydrogen bonds : angle 2.80147 ( 2226) covalent geometry : bond 0.00291 (13818) covalent geometry : angle 0.72537 (19208) Misc. bond : bond 0.00272 ( 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 219 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.213 Fit side-chains REVERT: E 17 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: J 17 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: N 7 MET cc_start: 0.7011 (ttt) cc_final: 0.6747 (ptm) REVERT: P 17 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: Q 53 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5495 (mttt) REVERT: R 17 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: V 17 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7426 (tm-30) outliers start: 29 outliers final: 17 residues processed: 207 average time/residue: 1.4643 time to fit residues: 325.8539 Evaluate side-chains 213 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 53 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 16 GLN 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 93 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.166647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153340 restraints weight = 9691.130| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 0.37 r_work: 0.3482 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1500 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= 0.124 Angle : 0.719 9.199 19208 Z= 0.263 Chirality : 0.038 0.114 2002 Planarity : 0.003 0.030 2324 Dihedral : 21.231 179.804 2283 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.20 % Allowed : 17.90 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.21), residues: 1274 helix: 4.01 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.91 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 9 HIS 0.005 0.001 HIS A 37 PHE 0.010 0.002 PHE I 42 ARG 0.006 0.000 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 817) hydrogen bonds : angle 2.76854 ( 2226) covalent geometry : bond 0.00280 (13818) covalent geometry : angle 0.71870 (19208) Misc. bond : bond 0.00258 ( 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 216 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.199 Fit side-chains REVERT: E 17 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: J 17 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: N 7 MET cc_start: 0.6944 (ttt) cc_final: 0.6656 (ptm) REVERT: P 17 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: Q 53 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5481 (mttt) REVERT: R 17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: V 17 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7426 (tm-30) outliers start: 25 outliers final: 16 residues processed: 206 average time/residue: 1.4468 time to fit residues: 320.8815 Evaluate side-chains 212 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 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 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 101 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.165664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152250 restraints weight = 9800.100| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 0.37 r_work: 0.3467 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1501 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= 0.135 Angle : 0.739 9.251 19208 Z= 0.273 Chirality : 0.039 0.117 2002 Planarity : 0.003 0.030 2324 Dihedral : 21.282 179.755 2283 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.56 % Allowed : 17.55 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.21), residues: 1274 helix: 3.93 (0.13), residues: 812 sheet: None (None), residues: 0 loop : 1.89 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 9 HIS 0.006 0.001 HIS A 37 PHE 0.011 0.002 PHE P 18 ARG 0.006 0.000 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 817) hydrogen bonds : angle 2.81273 ( 2226) covalent geometry : bond 0.00305 (13818) covalent geometry : angle 0.73873 (19208) Misc. bond : bond 0.00296 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10014.99 seconds wall clock time: 172 minutes 52.05 seconds (10372.05 seconds total)