Starting phenix.real_space_refine on Tue Mar 3 16:30:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.map" model { file = "/net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n2d_9327/03_2026/6n2d_9327.cif" } resolution = 3.3 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= 0.005 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4727 2.51 5 N 1201 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7162 Number of models: 1 Model: "" Number of chains: 13 Chain: "b2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 286 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "b1" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 320 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 1.60, per 1000 atoms: 0.22 Number of scatterers: 7162 At special positions: 0 Unit cell: (72.08, 97.52, 76.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1213 8.00 N 1201 7.00 C 4727 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=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 208.6 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'b2' and resid 10 through 29 Processing helix chain 'b2' and resid 29 through 43 Processing helix chain 'b1' and resid 9 through 49 removed outlier: 3.610A pdb=" N TYRb1 13 " --> pdb=" O GLYb1 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix Processing helix chain 'a' and resid 16 through 38 removed outlier: 3.582A pdb=" N MET a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 68 through 73 Processing helix chain 'a' and resid 75 through 92 removed outlier: 3.745A pdb=" N THR a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 130 Processing helix chain 'a' and resid 153 through 191 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 234 removed outlier: 4.263A pdb=" N MET a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'c0' and resid 3 through 37 Processing helix chain 'c0' and resid 40 through 72 removed outlier: 4.002A pdb=" N THRc0 47 " --> pdb=" O VALc0 43 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.923A pdb=" N PHEc0 67 " --> pdb=" O VALc0 63 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILEc0 68 " --> pdb=" O VALc0 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGc0 72 " --> pdb=" O ILEc0 68 " (cutoff:3.500A) Processing helix chain 'c1' and resid 3 through 37 Processing helix chain 'c1' and resid 40 through 72 removed outlier: 4.525A pdb=" N LEUc1 58 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) Proline residue: c1 59 - end of helix Processing helix chain 'c2' and resid 3 through 37 Processing helix chain 'c2' and resid 40 through 56 Processing helix chain 'c2' and resid 56 through 72 Processing helix chain 'c3' and resid 3 through 37 Processing helix chain 'c3' and resid 40 through 71 Proline residue: c3 59 - end of helix Processing helix chain 'c4' and resid 3 through 37 Processing helix chain 'c4' and resid 40 through 56 Processing helix chain 'c4' and resid 56 through 72 removed outlier: 4.032A pdb=" N ILEc4 68 " --> pdb=" O VALc4 64 " (cutoff:3.500A) Processing helix chain 'c5' and resid 3 through 37 Processing helix chain 'c5' and resid 40 through 72 removed outlier: 4.289A pdb=" N LEUc5 58 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 3 through 37 Processing helix chain 'c6' and resid 40 through 72 removed outlier: 4.373A pdb=" N LEUc6 58 " --> pdb=" O LEUc6 54 " (cutoff:3.500A) Proline residue: c6 59 - end of helix removed outlier: 3.635A pdb=" N GLYc6 71 " --> pdb=" O PHEc6 67 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGc6 72 " --> pdb=" O ILEc6 68 " (cutoff:3.500A) Processing helix chain 'c7' and resid 3 through 37 Processing helix chain 'c7' and resid 40 through 56 removed outlier: 3.665A pdb=" N LEUc7 44 " --> pdb=" O LEUc7 40 " (cutoff:3.500A) Processing helix chain 'c7' and resid 56 through 72 removed outlier: 3.504A pdb=" N ILEc7 60 " --> pdb=" O GLUc7 56 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 37 Processing helix chain 'c8' and resid 40 through 71 removed outlier: 4.938A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 3 through 37 removed outlier: 3.525A pdb=" N GLNc9 37 " --> pdb=" O GLYc9 33 " (cutoff:3.500A) Processing helix chain 'c9' and resid 40 through 71 removed outlier: 3.827A pdb=" N THRc9 47 " --> pdb=" O VALc9 43 " (cutoff:3.500A) Proline residue: c9 59 - end of helix 738 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2074 1.34 - 1.46: 1143 1.46 - 1.58: 4010 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 7268 Sorted by residual: bond pdb=" CG1 ILEc3 31 " pdb=" CD1 ILEc3 31 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 9.02e+00 bond pdb=" CG1 ILEc2 31 " pdb=" CD1 ILEc2 31 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.50e+00 bond pdb=" CG1 ILEc8 31 " pdb=" CD1 ILEc8 31 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.59e+00 bond pdb=" CG1 ILEc9 31 " pdb=" CD1 ILEc9 31 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.41e+00 bond pdb=" CG1 ILEc1 31 " pdb=" CD1 ILEc1 31 " ideal model delta sigma weight residual 1.513 1.419 0.094 3.90e-02 6.57e+02 5.83e+00 ... (remaining 7263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 9271 2.28 - 4.57: 514 4.57 - 6.85: 74 6.85 - 9.14: 19 9.14 - 11.42: 10 Bond angle restraints: 9888 Sorted by residual: angle pdb=" C SERc5 28 " pdb=" N ARGc5 29 " pdb=" CA ARGc5 29 " ideal model delta sigma weight residual 122.38 112.07 10.31 1.81e+00 3.05e-01 3.25e+01 angle pdb=" C ALAc0 57 " pdb=" N LEUc0 58 " pdb=" CA LEUc0 58 " ideal model delta sigma weight residual 121.80 111.35 10.45 2.44e+00 1.68e-01 1.83e+01 angle pdb=" N LEU a 76 " pdb=" CA LEU a 76 " pdb=" C LEU a 76 " ideal model delta sigma weight residual 111.28 115.74 -4.46 1.09e+00 8.42e-01 1.68e+01 angle pdb=" CA LEUc5 58 " pdb=" C LEUc5 58 " pdb=" N PROc5 59 " ideal model delta sigma weight residual 120.93 116.59 4.34 1.06e+00 8.90e-01 1.68e+01 angle pdb=" C ALAc3 57 " pdb=" N LEUc3 58 " pdb=" CA LEUc3 58 " ideal model delta sigma weight residual 121.80 111.88 9.92 2.44e+00 1.68e-01 1.65e+01 ... (remaining 9883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 3850 15.11 - 30.21: 259 30.21 - 45.32: 103 45.32 - 60.42: 4 60.42 - 75.53: 2 Dihedral angle restraints: 4218 sinusoidal: 1496 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ALAb2 29 " pdb=" C ALAb2 29 " pdb=" N TRPb2 30 " pdb=" CA TRPb2 30 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PHEb1 28 " pdb=" C PHEb1 28 " pdb=" N ALAb1 29 " pdb=" CA ALAb1 29 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TRPb2 30 " pdb=" C TRPb2 30 " pdb=" N GLNb2 31 " pdb=" CA GLNb2 31 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 912 0.066 - 0.132: 285 0.132 - 0.198: 58 0.198 - 0.264: 7 0.264 - 0.330: 4 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILEc9 10 " pdb=" CA ILEc9 10 " pdb=" CG1 ILEc9 10 " pdb=" CG2 ILEc9 10 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILEb1 11 " pdb=" CA ILEb1 11 " pdb=" CG1 ILEb1 11 " pdb=" CG2 ILEb1 11 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ARGc5 29 " pdb=" N ARGc5 29 " pdb=" C ARGc5 29 " pdb=" CB ARGc5 29 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1263 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUc1 58 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PROc1 59 " -0.133 5.00e-02 4.00e+02 pdb=" CA PROc1 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PROc1 59 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUc3 58 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PROc3 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROc3 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROc3 59 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLNc9 37 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PROc9 38 " -0.127 5.00e-02 4.00e+02 pdb=" CA PROc9 38 " 0.038 5.00e-02 4.00e+02 pdb=" CD PROc9 38 " 0.040 5.00e-02 4.00e+02 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 3 2.27 - 2.93: 2752 2.93 - 3.58: 11899 3.58 - 4.24: 16811 4.24 - 4.90: 28398 Nonbonded interactions: 59863 Sorted by model distance: nonbonded pdb=" O PHEc6 65 " pdb=" CD2 TYRc6 69 " model vdw 1.610 3.340 nonbonded pdb=" O LEU a 180 " pdb=" CD1 LEU a 184 " model vdw 1.633 3.460 nonbonded pdb=" O ALAc5 57 " pdb=" CD1 ILEc5 61 " model vdw 1.755 3.460 nonbonded pdb=" O VALc1 63 " pdb=" OG SERc1 66 " model vdw 2.280 3.040 nonbonded pdb=" O VALc3 63 " pdb=" OG SERc3 66 " model vdw 2.299 3.040 ... (remaining 59858 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 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43)) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 43)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.008 0.117 7268 Z= 0.320 Angle : 1.207 11.420 9888 Z= 0.642 Chirality : 0.066 0.330 1266 Planarity : 0.010 0.077 1220 Dihedral : 11.746 75.526 2492 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.71 % Allowed : 12.71 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.22), residues: 963 helix: -1.50 (0.14), residues: 892 sheet: None (None), residues: 0 loop : -3.52 (0.57), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGc1 29 TYR 0.034 0.004 TYRc0 69 PHE 0.043 0.004 PHEc6 65 TRP 0.023 0.002 TRP a 206 HIS 0.003 0.001 HISb2 43 Details of bonding type rmsd covalent geometry : bond 0.00768 ( 7268) covalent geometry : angle 1.20668 ( 9888) hydrogen bonds : bond 0.10811 ( 738) hydrogen bonds : angle 5.79506 ( 2214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: c2 29 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7896 (mmm-85) REVERT: c3 12 VAL cc_start: 0.8653 (t) cc_final: 0.8383 (t) REVERT: c5 72 ARG cc_start: 0.6182 (tpp80) cc_final: 0.5928 (tpp-160) REVERT: c6 32 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7288 (tm-30) REVERT: c7 48 MET cc_start: 0.8170 (tmm) cc_final: 0.7949 (tmm) outliers start: 5 outliers final: 0 residues processed: 265 average time/residue: 0.0948 time to fit residues: 32.1745 Evaluate side-chains 210 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN a 16 ASN a 90 ASN a 173 ASN a 207 GLN a 217 GLN c4 45 GLN c5 23 ASN ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 23 ASN c9 45 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126464 restraints weight = 8796.779| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.36 r_work: 0.3580 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7268 Z= 0.175 Angle : 0.753 10.300 9888 Z= 0.386 Chirality : 0.044 0.215 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.502 20.490 1043 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 8.33 % Allowed : 18.50 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 963 helix: 0.33 (0.16), residues: 892 sheet: None (None), residues: 0 loop : -2.66 (0.67), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGc0 72 TYR 0.040 0.002 TYRc6 69 PHE 0.023 0.002 PHE a 87 TRP 0.014 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7268) covalent geometry : angle 0.75288 ( 9888) hydrogen bonds : bond 0.05146 ( 738) hydrogen bonds : angle 4.35981 ( 2214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 0.262 Fit side-chains REVERT: b1 17 MET cc_start: 0.8886 (mmm) cc_final: 0.8453 (mmm) REVERT: a 17 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8219 (tm) REVERT: a 85 TYR cc_start: 0.7637 (t80) cc_final: 0.7435 (t80) REVERT: a 203 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8017 (tmm) REVERT: a 210 SER cc_start: 0.8953 (t) cc_final: 0.8440 (m) REVERT: c2 37 GLN cc_start: 0.7978 (mt0) cc_final: 0.7751 (mt0) REVERT: c3 12 VAL cc_start: 0.8415 (t) cc_final: 0.8169 (t) REVERT: c4 31 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8675 (tt) REVERT: c5 6 LEU cc_start: 0.8594 (tt) cc_final: 0.8381 (tp) REVERT: c5 67 PHE cc_start: 0.8665 (m-80) cc_final: 0.7790 (m-80) REVERT: c5 72 ARG cc_start: 0.5698 (tpp80) cc_final: 0.5432 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7707 (tm-30) REVERT: c6 37 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8291 (tm-30) REVERT: c6 65 PHE cc_start: 0.8721 (m-10) cc_final: 0.8489 (m-80) REVERT: c6 72 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7425 (ttm110) REVERT: c7 30 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8851 (m) REVERT: c7 58 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (tt) REVERT: c7 72 ARG cc_start: 0.6199 (ttm170) cc_final: 0.5875 (ttm170) outliers start: 59 outliers final: 29 residues processed: 255 average time/residue: 0.0840 time to fit residues: 28.0561 Evaluate side-chains 234 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 68 ILE Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 60 ILE Chi-restraints excluded: chain c5 residue 63 VAL Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 58 LEU Chi-restraints excluded: chain c7 residue 67 PHE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 99 HIS a 207 GLN ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122408 restraints weight = 8824.212| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.35 r_work: 0.3531 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7268 Z= 0.181 Angle : 0.749 10.040 9888 Z= 0.379 Chirality : 0.045 0.216 1266 Planarity : 0.007 0.062 1220 Dihedral : 4.306 18.102 1043 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 9.46 % Allowed : 22.74 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 963 helix: 1.03 (0.17), residues: 889 sheet: None (None), residues: 0 loop : -2.19 (0.75), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGc0 72 TYR 0.031 0.002 TYRc6 69 PHE 0.024 0.002 PHE a 87 TRP 0.020 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7268) covalent geometry : angle 0.74940 ( 9888) hydrogen bonds : bond 0.05023 ( 738) hydrogen bonds : angle 4.22334 ( 2214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7487 (tttm) cc_final: 0.7015 (tttt) REVERT: b2 36 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7705 (tt) REVERT: b1 17 MET cc_start: 0.8874 (mmm) cc_final: 0.8634 (mmm) REVERT: a 17 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8097 (tm) REVERT: a 63 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8864 (tp) REVERT: a 207 GLN cc_start: 0.8958 (tt0) cc_final: 0.8753 (tt0) REVERT: a 210 SER cc_start: 0.9045 (t) cc_final: 0.8643 (m) REVERT: c0 32 GLU cc_start: 0.8271 (tt0) cc_final: 0.7985 (tt0) REVERT: c2 37 GLN cc_start: 0.7985 (mt0) cc_final: 0.7737 (mt0) REVERT: c2 54 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9006 (mp) REVERT: c3 12 VAL cc_start: 0.8397 (t) cc_final: 0.8166 (t) REVERT: c4 31 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (tt) REVERT: c5 72 ARG cc_start: 0.5805 (tpp80) cc_final: 0.5514 (tpp-160) REVERT: c6 29 ARG cc_start: 0.8993 (mtt-85) cc_final: 0.8728 (mtp85) REVERT: c6 32 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7808 (tm-30) REVERT: c6 48 MET cc_start: 0.8481 (ttp) cc_final: 0.8246 (ttp) REVERT: c6 72 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7601 (ttm110) REVERT: c7 72 ARG cc_start: 0.6169 (ttm170) cc_final: 0.5872 (ttm170) REVERT: c8 14 LEU cc_start: 0.8781 (mt) cc_final: 0.8531 (mt) outliers start: 67 outliers final: 37 residues processed: 260 average time/residue: 0.0860 time to fit residues: 29.4328 Evaluate side-chains 257 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 19 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 54 LEU Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c7 residue 67 PHE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120538 restraints weight = 8899.024| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.12 r_work: 0.3503 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7268 Z= 0.172 Angle : 0.733 9.412 9888 Z= 0.369 Chirality : 0.045 0.215 1266 Planarity : 0.006 0.062 1220 Dihedral : 4.197 16.421 1043 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 8.62 % Allowed : 24.86 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.27), residues: 963 helix: 1.41 (0.17), residues: 889 sheet: None (None), residues: 0 loop : -1.97 (0.78), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGc0 72 TYR 0.024 0.002 TYRc6 69 PHE 0.020 0.002 PHE a 56 TRP 0.020 0.002 TRP a 206 HIS 0.012 0.002 HIS a 99 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7268) covalent geometry : angle 0.73320 ( 9888) hydrogen bonds : bond 0.04881 ( 738) hydrogen bonds : angle 4.12573 ( 2214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7471 (tttm) cc_final: 0.6965 (tttt) REVERT: b2 36 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (tt) REVERT: a 17 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8055 (tm) REVERT: a 210 SER cc_start: 0.9121 (t) cc_final: 0.8712 (m) REVERT: a 232 LYS cc_start: 0.9167 (tttt) cc_final: 0.8673 (ttpt) REVERT: c1 32 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: c1 48 MET cc_start: 0.8293 (ttp) cc_final: 0.7803 (ttm) REVERT: c3 12 VAL cc_start: 0.8537 (t) cc_final: 0.8270 (t) REVERT: c4 31 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8747 (tt) REVERT: c5 67 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: c5 72 ARG cc_start: 0.6103 (tpp80) cc_final: 0.5790 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8031 (tm-30) REVERT: c6 37 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8213 (tm-30) REVERT: c6 56 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8096 (mm-30) REVERT: c6 72 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7746 (ttm110) REVERT: c8 14 LEU cc_start: 0.8979 (mt) cc_final: 0.8740 (mt) REVERT: c9 30 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9021 (m) outliers start: 61 outliers final: 36 residues processed: 257 average time/residue: 0.0844 time to fit residues: 28.5462 Evaluate side-chains 259 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c5 residue 67 PHE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c7 residue 67 PHE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.148742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117070 restraints weight = 9225.271| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.20 r_work: 0.3467 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7268 Z= 0.182 Angle : 0.731 9.906 9888 Z= 0.370 Chirality : 0.045 0.213 1266 Planarity : 0.006 0.063 1220 Dihedral : 4.110 14.474 1043 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 9.75 % Allowed : 25.14 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 963 helix: 1.51 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.92 (0.90), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGc3 72 TYR 0.041 0.002 TYRc7 69 PHE 0.023 0.001 PHE a 87 TRP 0.024 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7268) covalent geometry : angle 0.73077 ( 9888) hydrogen bonds : bond 0.04944 ( 738) hydrogen bonds : angle 4.15155 ( 2214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7484 (tttm) cc_final: 0.7208 (tmtt) REVERT: a 17 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (tm) REVERT: a 63 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (tp) REVERT: a 117 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8114 (mm) REVERT: a 174 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8675 (mm) REVERT: a 210 SER cc_start: 0.9103 (t) cc_final: 0.8720 (m) REVERT: a 228 TYR cc_start: 0.8960 (m-80) cc_final: 0.8747 (m-80) REVERT: c0 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8326 (mmt180) REVERT: c0 69 TYR cc_start: 0.8395 (m-80) cc_final: 0.8173 (m-80) REVERT: c1 32 GLU cc_start: 0.9110 (pp20) cc_final: 0.8569 (tt0) REVERT: c3 12 VAL cc_start: 0.8480 (t) cc_final: 0.8202 (t) REVERT: c4 31 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (tt) REVERT: c5 72 ARG cc_start: 0.6237 (tpp80) cc_final: 0.5887 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7982 (tm-30) REVERT: c6 72 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7739 (ttm110) REVERT: c8 14 LEU cc_start: 0.8886 (mt) cc_final: 0.8681 (mt) REVERT: c9 30 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9022 (m) outliers start: 69 outliers final: 44 residues processed: 262 average time/residue: 0.0910 time to fit residues: 31.1942 Evaluate side-chains 271 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 19 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c3 residue 68 ILE Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117238 restraints weight = 9220.962| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.22 r_work: 0.3461 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7268 Z= 0.179 Angle : 0.735 9.796 9888 Z= 0.370 Chirality : 0.045 0.212 1266 Planarity : 0.007 0.064 1220 Dihedral : 4.123 15.015 1043 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 9.46 % Allowed : 25.85 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 963 helix: 1.57 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.83 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGc0 72 TYR 0.042 0.002 TYRc7 69 PHE 0.018 0.001 PHEc5 67 TRP 0.021 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 7268) covalent geometry : angle 0.73523 ( 9888) hydrogen bonds : bond 0.04846 ( 738) hydrogen bonds : angle 4.15736 ( 2214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7472 (tttm) cc_final: 0.7252 (tmtt) REVERT: a 17 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8031 (tm) REVERT: a 63 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8941 (tp) REVERT: a 117 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8061 (mm) REVERT: a 210 SER cc_start: 0.9148 (t) cc_final: 0.8728 (m) REVERT: c0 29 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.8227 (mmp80) REVERT: c0 58 LEU cc_start: 0.7256 (tt) cc_final: 0.7050 (tt) REVERT: c1 32 GLU cc_start: 0.9100 (pp20) cc_final: 0.8565 (tt0) REVERT: c1 48 MET cc_start: 0.8153 (ttp) cc_final: 0.7728 (ttm) REVERT: c2 37 GLN cc_start: 0.8002 (mt0) cc_final: 0.7760 (mt0) REVERT: c3 12 VAL cc_start: 0.8458 (t) cc_final: 0.8174 (t) REVERT: c4 31 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8704 (tt) REVERT: c5 29 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (ptp-110) REVERT: c5 72 ARG cc_start: 0.6239 (tpp80) cc_final: 0.5948 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8054 (tm-30) REVERT: c6 37 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8083 (tm-30) REVERT: c6 72 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7685 (ttm110) REVERT: c9 30 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9012 (m) outliers start: 67 outliers final: 44 residues processed: 250 average time/residue: 0.0870 time to fit residues: 28.7485 Evaluate side-chains 261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 29 ARG Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 173 ASN ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116011 restraints weight = 9275.974| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.23 r_work: 0.3450 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7268 Z= 0.182 Angle : 0.742 9.868 9888 Z= 0.372 Chirality : 0.045 0.211 1266 Planarity : 0.006 0.065 1220 Dihedral : 4.097 13.621 1043 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 9.32 % Allowed : 26.84 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.27), residues: 963 helix: 1.62 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.78 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGc0 72 TYR 0.043 0.002 TYRc7 69 PHE 0.015 0.002 PHE a 96 TRP 0.020 0.001 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7268) covalent geometry : angle 0.74232 ( 9888) hydrogen bonds : bond 0.04879 ( 738) hydrogen bonds : angle 4.19815 ( 2214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7549 (tttm) cc_final: 0.7336 (tmtt) REVERT: b1 11 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8462 (mt) REVERT: a 17 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8005 (tm) REVERT: a 63 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8938 (tp) REVERT: a 117 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (mm) REVERT: a 210 SER cc_start: 0.9103 (t) cc_final: 0.8656 (m) REVERT: c0 29 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.8082 (mmp80) REVERT: c1 32 GLU cc_start: 0.9068 (pp20) cc_final: 0.8595 (tt0) REVERT: c1 48 MET cc_start: 0.8197 (ttp) cc_final: 0.7752 (ttm) REVERT: c2 37 GLN cc_start: 0.8032 (mt0) cc_final: 0.7806 (mt0) REVERT: c3 12 VAL cc_start: 0.8526 (t) cc_final: 0.8276 (t) REVERT: c5 29 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8689 (ptp-110) REVERT: c5 72 ARG cc_start: 0.6231 (tpp80) cc_final: 0.5932 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8043 (tm-30) REVERT: c6 37 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8105 (tm-30) REVERT: c6 72 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7781 (ttm110) REVERT: c7 72 ARG cc_start: 0.6132 (ttm170) cc_final: 0.5926 (ttm170) REVERT: c9 30 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.9018 (m) outliers start: 66 outliers final: 46 residues processed: 260 average time/residue: 0.0853 time to fit residues: 29.1376 Evaluate side-chains 272 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 19 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c3 residue 68 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 5 VAL Chi-restraints excluded: chain c5 residue 29 ARG Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.146799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114894 restraints weight = 9309.941| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.23 r_work: 0.3433 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7268 Z= 0.189 Angle : 0.755 9.967 9888 Z= 0.380 Chirality : 0.045 0.211 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.116 14.110 1043 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 9.60 % Allowed : 26.84 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.27), residues: 963 helix: 1.61 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.75 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGc0 72 TYR 0.046 0.002 TYRc7 69 PHE 0.016 0.002 PHEc8 65 TRP 0.026 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7268) covalent geometry : angle 0.75468 ( 9888) hydrogen bonds : bond 0.04954 ( 738) hydrogen bonds : angle 4.22792 ( 2214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7528 (tttm) cc_final: 0.7298 (tmtt) REVERT: b1 11 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8468 (mt) REVERT: a 17 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8000 (tm) REVERT: a 63 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8946 (tp) REVERT: a 90 ASN cc_start: 0.8922 (t0) cc_final: 0.8631 (t0) REVERT: a 117 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8052 (mm) REVERT: a 210 SER cc_start: 0.9115 (t) cc_final: 0.8672 (m) REVERT: a 228 TYR cc_start: 0.8914 (m-80) cc_final: 0.8684 (m-80) REVERT: c0 29 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8136 (mmp80) REVERT: c0 69 TYR cc_start: 0.8459 (m-80) cc_final: 0.8106 (m-80) REVERT: c1 32 GLU cc_start: 0.9067 (pp20) cc_final: 0.8590 (tt0) REVERT: c1 48 MET cc_start: 0.8208 (ttp) cc_final: 0.7759 (ttm) REVERT: c2 37 GLN cc_start: 0.8066 (mt0) cc_final: 0.7820 (mt0) REVERT: c3 12 VAL cc_start: 0.8501 (t) cc_final: 0.8243 (t) REVERT: c5 37 GLN cc_start: 0.7875 (pp30) cc_final: 0.7580 (pp30) REVERT: c5 72 ARG cc_start: 0.6259 (tpp80) cc_final: 0.5979 (tpp-160) REVERT: c6 29 ARG cc_start: 0.9037 (mtt-85) cc_final: 0.8776 (mtp180) REVERT: c6 32 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8051 (tm-30) REVERT: c6 37 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8119 (tm-30) REVERT: c7 72 ARG cc_start: 0.6028 (ttm170) cc_final: 0.5809 (ttm170) REVERT: c9 30 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9020 (m) outliers start: 68 outliers final: 52 residues processed: 259 average time/residue: 0.0832 time to fit residues: 28.2971 Evaluate side-chains 279 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 19 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 50 ASN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c3 residue 68 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 5 VAL Chi-restraints excluded: chain c5 residue 30 THR Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117402 restraints weight = 9208.914| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.23 r_work: 0.3464 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7268 Z= 0.173 Angle : 0.747 10.935 9888 Z= 0.371 Chirality : 0.045 0.218 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.114 14.068 1043 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 8.90 % Allowed : 26.98 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.27), residues: 963 helix: 1.67 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.73 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGc0 72 TYR 0.044 0.002 TYRc7 69 PHE 0.019 0.002 PHE a 87 TRP 0.024 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7268) covalent geometry : angle 0.74672 ( 9888) hydrogen bonds : bond 0.04821 ( 738) hydrogen bonds : angle 4.17236 ( 2214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7553 (tttm) cc_final: 0.7235 (tmtt) REVERT: b1 11 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8431 (mt) REVERT: a 17 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7858 (tm) REVERT: a 63 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8938 (tp) REVERT: a 91 MET cc_start: 0.8808 (ptp) cc_final: 0.8444 (ptp) REVERT: a 117 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8004 (mm) REVERT: a 210 SER cc_start: 0.9109 (t) cc_final: 0.8702 (m) REVERT: c0 29 ARG cc_start: 0.8540 (mmt-90) cc_final: 0.8127 (mmp80) REVERT: c0 69 TYR cc_start: 0.8486 (m-80) cc_final: 0.8084 (m-80) REVERT: c1 32 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: c1 37 GLN cc_start: 0.7939 (pm20) cc_final: 0.7467 (pm20) REVERT: c1 48 MET cc_start: 0.8148 (ttp) cc_final: 0.7684 (ttm) REVERT: c2 37 GLN cc_start: 0.8025 (mt0) cc_final: 0.7785 (mt0) REVERT: c3 12 VAL cc_start: 0.8436 (t) cc_final: 0.8170 (t) REVERT: c3 36 ARG cc_start: 0.8801 (ttm170) cc_final: 0.8563 (ttm-80) REVERT: c5 37 GLN cc_start: 0.7814 (pp30) cc_final: 0.7547 (pp30) REVERT: c5 72 ARG cc_start: 0.6228 (tpp80) cc_final: 0.5943 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8099 (tm-30) REVERT: c6 37 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8259 (tm-30) REVERT: c6 61 ILE cc_start: 0.9098 (mm) cc_final: 0.8837 (mt) REVERT: c9 30 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8953 (m) outliers start: 63 outliers final: 48 residues processed: 253 average time/residue: 0.0825 time to fit residues: 27.4695 Evaluate side-chains 268 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 66 SER Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 61 ILE Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 5 VAL Chi-restraints excluded: chain c5 residue 30 THR Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115541 restraints weight = 9357.020| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.25 r_work: 0.3433 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7268 Z= 0.191 Angle : 0.776 10.583 9888 Z= 0.389 Chirality : 0.046 0.219 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.147 13.846 1043 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 9.04 % Allowed : 26.98 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 963 helix: 1.59 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.75 (0.89), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGc0 72 TYR 0.046 0.002 TYRc7 69 PHE 0.023 0.002 PHEc6 65 TRP 0.023 0.001 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7268) covalent geometry : angle 0.77587 ( 9888) hydrogen bonds : bond 0.04979 ( 738) hydrogen bonds : angle 4.25230 ( 2214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7454 (tttm) cc_final: 0.7235 (tmtt) REVERT: b1 11 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (mt) REVERT: a 17 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7866 (tm) REVERT: a 117 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8004 (mm) REVERT: a 210 SER cc_start: 0.9138 (t) cc_final: 0.8732 (m) REVERT: c0 29 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8121 (mmp80) REVERT: c0 69 TYR cc_start: 0.8503 (m-80) cc_final: 0.8080 (m-80) REVERT: c1 32 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: c1 37 GLN cc_start: 0.7969 (pm20) cc_final: 0.7497 (pm20) REVERT: c1 48 MET cc_start: 0.8212 (ttp) cc_final: 0.7756 (ttm) REVERT: c2 37 GLN cc_start: 0.8021 (mt0) cc_final: 0.7790 (mt0) REVERT: c3 12 VAL cc_start: 0.8538 (t) cc_final: 0.8289 (t) REVERT: c4 48 MET cc_start: 0.9165 (ttp) cc_final: 0.8881 (ttt) REVERT: c5 37 GLN cc_start: 0.7859 (pp30) cc_final: 0.7576 (pp30) REVERT: c5 72 ARG cc_start: 0.6272 (tpp80) cc_final: 0.5982 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8119 (tm-30) REVERT: c6 37 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8251 (tm-30) REVERT: c9 37 GLN cc_start: 0.7931 (pp30) cc_final: 0.7668 (pp30) outliers start: 64 outliers final: 51 residues processed: 259 average time/residue: 0.0785 time to fit residues: 26.9044 Evaluate side-chains 275 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 90 ASN Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 121 VAL Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 61 ILE Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 5 VAL Chi-restraints excluded: chain c5 residue 30 THR Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** c3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114893 restraints weight = 9250.430| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.32 r_work: 0.3416 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7268 Z= 0.194 Angle : 0.782 10.268 9888 Z= 0.392 Chirality : 0.047 0.223 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.149 13.729 1043 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 8.47 % Allowed : 27.97 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 963 helix: 1.57 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.75 (0.85), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGc0 72 TYR 0.047 0.002 TYRc7 69 PHE 0.039 0.002 PHE a 87 TRP 0.023 0.001 TRP a 206 HIS 0.005 0.001 HIS a 128 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7268) covalent geometry : angle 0.78169 ( 9888) hydrogen bonds : bond 0.05006 ( 738) hydrogen bonds : angle 4.28438 ( 2214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.71 seconds wall clock time: 26 minutes 38.40 seconds (1598.40 seconds total)