Starting phenix.real_space_refine on Mon Apr 28 06:10:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n2d_9327/04_2025/6n2d_9327.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n2d_9327/04_2025/6n2d_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_9327/04_2025/6n2d_9327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n2d_9327/04_2025/6n2d_9327.map" model { file = "/net/cci-nas-00/data/ceres_data/6n2d_9327/04_2025/6n2d_9327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n2d_9327/04_2025/6n2d_9327.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} 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: 5.17, per 1000 atoms: 0.72 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.65 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: 2.12 Time building geometry restraints manager: 2.10 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: 1.520 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP a 206 HIS 0.003 0.001 HISb2 43 PHE 0.043 0.004 PHEc6 65 TYR 0.034 0.004 TYRc0 69 ARG 0.008 0.001 ARGc1 29 Details of bonding type rmsd hydrogen bonds : bond 0.10811 ( 738) hydrogen bonds : angle 5.79506 ( 2214) covalent geometry : bond 0.00768 ( 7268) covalent geometry : angle 1.20668 ( 9888) *********************** 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 : 0.726 Fit side-chains revert: symmetry clash REVERT: c2 29 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7895 (mmm-85) REVERT: c3 12 VAL cc_start: 0.8654 (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: 0.7951 (tmm) outliers start: 5 outliers final: 0 residues processed: 265 average time/residue: 0.2281 time to fit residues: 76.6566 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 : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.157824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126930 restraints weight = 8561.512| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.32 r_work: 0.3593 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2331 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= 0.168 Angle : 0.748 10.247 9888 Z= 0.383 Chirality : 0.044 0.214 1266 Planarity : 0.007 0.065 1220 Dihedral : 4.488 20.494 1043 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 8.05 % Allowed : 18.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 963 helix: 0.36 (0.16), residues: 892 sheet: None (None), residues: 0 loop : -2.66 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 206 HIS 0.006 0.001 HIS a 128 PHE 0.022 0.002 PHE a 87 TYR 0.043 0.002 TYRc6 69 ARG 0.008 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 738) hydrogen bonds : angle 4.33778 ( 2214) covalent geometry : bond 0.00377 ( 7268) covalent geometry : angle 0.74818 ( 9888) *********************** 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 279 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: b2 36 ILE cc_start: 0.7878 (tt) cc_final: 0.7624 (tt) REVERT: b1 17 MET cc_start: 0.8887 (mmm) cc_final: 0.8448 (mmm) REVERT: a 17 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8134 (tm) REVERT: a 56 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: a 203 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.8021 (tmm) REVERT: a 210 SER cc_start: 0.8960 (t) cc_final: 0.8444 (m) REVERT: c2 29 ARG cc_start: 0.8383 (mmt90) cc_final: 0.8147 (mmt180) REVERT: c2 37 GLN cc_start: 0.7961 (mt0) cc_final: 0.7741 (mt0) REVERT: c3 12 VAL cc_start: 0.8405 (t) cc_final: 0.8163 (t) REVERT: c4 31 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8664 (tt) REVERT: c5 6 LEU cc_start: 0.8589 (tt) cc_final: 0.8374 (tp) REVERT: c5 67 PHE cc_start: 0.8666 (m-80) cc_final: 0.7822 (m-80) REVERT: c5 72 ARG cc_start: 0.5681 (tpp80) cc_final: 0.5413 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7707 (tm-30) REVERT: c6 37 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8302 (tm-30) REVERT: c6 65 PHE cc_start: 0.8729 (m-10) cc_final: 0.8505 (m-80) REVERT: c6 72 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7439 (ttm110) REVERT: c7 30 THR cc_start: 0.9093 (t) cc_final: 0.8838 (m) REVERT: c7 58 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7830 (tt) REVERT: c7 72 ARG cc_start: 0.6175 (ttm170) cc_final: 0.5852 (ttm170) outliers start: 57 outliers final: 28 residues processed: 255 average time/residue: 0.1952 time to fit residues: 64.7247 Evaluate side-chains 232 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain c7 residue 67 PHE Chi-restraints excluded: chain c8 residue 67 PHE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 173 ASN a 207 GLN a 217 GLN ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126346 restraints weight = 8720.819| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.34 r_work: 0.3576 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7268 Z= 0.161 Angle : 0.729 9.316 9888 Z= 0.365 Chirality : 0.044 0.211 1266 Planarity : 0.007 0.062 1220 Dihedral : 4.304 18.318 1043 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 9.32 % Allowed : 22.46 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 963 helix: 1.13 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -2.94 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.024 0.001 PHE a 87 TYR 0.031 0.002 TYRc6 69 ARG 0.008 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 738) hydrogen bonds : angle 4.12683 ( 2214) covalent geometry : bond 0.00367 ( 7268) covalent geometry : angle 0.72885 ( 9888) *********************** 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 287 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7310 (tttm) cc_final: 0.6822 (tttt) REVERT: b2 36 ILE cc_start: 0.7795 (tt) cc_final: 0.7593 (tt) REVERT: b1 17 MET cc_start: 0.8834 (mmm) cc_final: 0.8615 (mmm) REVERT: a 17 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8011 (tm) REVERT: a 63 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8837 (tp) REVERT: a 85 TYR cc_start: 0.7612 (t80) cc_final: 0.7256 (t80) REVERT: a 207 GLN cc_start: 0.8946 (tt0) cc_final: 0.8712 (tt0) REVERT: a 210 SER cc_start: 0.8998 (t) cc_final: 0.8607 (m) REVERT: a 232 LYS cc_start: 0.9011 (tttt) cc_final: 0.8466 (ttpt) REVERT: c0 32 GLU cc_start: 0.8217 (tt0) cc_final: 0.7960 (tt0) REVERT: c2 54 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8982 (mp) REVERT: c3 12 VAL cc_start: 0.8338 (t) cc_final: 0.8067 (t) REVERT: c5 6 LEU cc_start: 0.8597 (tt) cc_final: 0.8378 (tp) REVERT: c5 48 MET cc_start: 0.8717 (ttp) cc_final: 0.7647 (ttp) REVERT: c5 72 ARG cc_start: 0.5873 (tpp80) cc_final: 0.5598 (tpp-160) REVERT: c6 29 ARG cc_start: 0.8960 (mtt-85) cc_final: 0.8676 (mtp85) REVERT: c6 32 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7785 (tm-30) REVERT: c6 72 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: c8 14 LEU cc_start: 0.8763 (mt) cc_final: 0.8497 (mt) REVERT: c9 30 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8818 (m) outliers start: 66 outliers final: 34 residues processed: 258 average time/residue: 0.1905 time to fit residues: 64.2078 Evaluate side-chains 249 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 c2 residue 54 LEU 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 68 ILE Chi-restraints excluded: chain c6 residue 6 LEU 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 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 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 6 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118474 restraints weight = 9121.086| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.30 r_work: 0.3467 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3183 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 : 0.750 9.681 9888 Z= 0.375 Chirality : 0.045 0.216 1266 Planarity : 0.007 0.062 1220 Dihedral : 4.164 15.070 1043 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 8.47 % Allowed : 24.58 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 963 helix: 1.41 (0.17), residues: 891 sheet: None (None), residues: 0 loop : -1.94 (0.80), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.018 0.002 PHE a 56 TYR 0.024 0.002 TYRc6 69 ARG 0.005 0.001 ARGc3 72 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 738) hydrogen bonds : angle 4.14362 ( 2214) covalent geometry : bond 0.00428 ( 7268) covalent geometry : angle 0.74979 ( 9888) *********************** 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 282 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7417 (tttm) cc_final: 0.7119 (tmtt) REVERT: a 17 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (tm) REVERT: a 56 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: a 207 GLN cc_start: 0.8998 (tt0) cc_final: 0.8758 (tt0) REVERT: a 210 SER cc_start: 0.9082 (t) cc_final: 0.8676 (m) REVERT: c0 29 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8160 (mmt180) REVERT: c1 32 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: c1 48 MET cc_start: 0.8177 (ttp) cc_final: 0.7695 (ttm) REVERT: c3 12 VAL cc_start: 0.8448 (t) cc_final: 0.8179 (t) REVERT: c3 48 MET cc_start: 0.9083 (ttp) cc_final: 0.8848 (ttt) REVERT: c5 6 LEU cc_start: 0.8726 (tt) cc_final: 0.8444 (tp) REVERT: c5 67 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: c5 72 ARG cc_start: 0.6069 (tpp80) cc_final: 0.5721 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7932 (tm-30) REVERT: c6 48 MET cc_start: 0.8606 (ttp) cc_final: 0.8398 (ttp) REVERT: c6 56 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8054 (mm-30) REVERT: c6 72 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7688 (ttm110) REVERT: c8 14 LEU cc_start: 0.8884 (mt) cc_final: 0.8649 (mt) REVERT: c9 30 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8999 (m) outliers start: 60 outliers final: 41 residues processed: 252 average time/residue: 0.2052 time to fit residues: 67.3926 Evaluate side-chains 258 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 56 PHE 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 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 32 GLU Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 c7 residue 52 VAL Chi-restraints excluded: chain c7 residue 67 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS a 173 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118069 restraints weight = 9090.836| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.28 r_work: 0.3458 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3407 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= 0.177 Angle : 0.736 9.725 9888 Z= 0.369 Chirality : 0.045 0.214 1266 Planarity : 0.006 0.063 1220 Dihedral : 4.100 15.059 1043 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 9.89 % Allowed : 24.86 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 963 helix: 1.52 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.88 (0.88), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.028 0.002 PHE a 87 TYR 0.038 0.002 TYRc7 69 ARG 0.006 0.001 ARGc3 72 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 738) hydrogen bonds : angle 4.12446 ( 2214) covalent geometry : bond 0.00420 ( 7268) covalent geometry : angle 0.73617 ( 9888) *********************** 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 295 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 225 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7393 (tttm) cc_final: 0.7151 (tmtt) REVERT: a 17 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8029 (tm) REVERT: a 63 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8947 (tp) REVERT: a 210 SER cc_start: 0.9107 (t) cc_final: 0.8714 (m) REVERT: c0 58 LEU cc_start: 0.7300 (tt) cc_final: 0.7075 (tt) REVERT: c0 69 TYR cc_start: 0.8404 (m-80) cc_final: 0.8201 (m-80) REVERT: c1 32 GLU cc_start: 0.9121 (pp20) cc_final: 0.8587 (tt0) REVERT: c2 32 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: c3 12 VAL cc_start: 0.8458 (t) cc_final: 0.8177 (t) REVERT: c5 6 LEU cc_start: 0.8739 (tt) cc_final: 0.8458 (tp) REVERT: c5 72 ARG cc_start: 0.6116 (tpp80) cc_final: 0.5752 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8040 (tm-30) REVERT: c6 72 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7621 (ttm110) REVERT: c8 14 LEU cc_start: 0.8871 (mt) cc_final: 0.8662 (mt) REVERT: c9 30 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9018 (m) outliers start: 70 outliers final: 46 residues processed: 260 average time/residue: 0.2034 time to fit residues: 68.2649 Evaluate side-chains 268 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 56 PHE 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 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 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 32 GLU 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 32 GLU Chi-restraints excluded: chain c4 residue 45 GLN Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c5 residue 30 THR Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 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 92 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS a 173 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116269 restraints weight = 9171.854| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.21 r_work: 0.3440 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3519 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= 0.188 Angle : 0.752 9.934 9888 Z= 0.377 Chirality : 0.045 0.213 1266 Planarity : 0.007 0.065 1220 Dihedral : 4.103 14.560 1043 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 10.45 % Allowed : 25.00 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 963 helix: 1.50 (0.16), residues: 897 sheet: None (None), residues: 0 loop : -1.79 (0.90), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.023 0.002 PHEc5 67 TYR 0.042 0.002 TYRc7 69 ARG 0.011 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 738) hydrogen bonds : angle 4.18398 ( 2214) covalent geometry : bond 0.00452 ( 7268) covalent geometry : angle 0.75181 ( 9888) *********************** 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 293 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7464 (tttm) cc_final: 0.7228 (tmtt) REVERT: a 17 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (tm) REVERT: a 63 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8971 (tp) REVERT: a 91 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (mpp) REVERT: a 174 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8548 (mm) REVERT: a 210 SER cc_start: 0.9156 (t) cc_final: 0.8735 (m) REVERT: c0 69 TYR cc_start: 0.8421 (m-80) cc_final: 0.8204 (m-80) REVERT: c1 32 GLU cc_start: 0.9119 (pp20) cc_final: 0.8555 (tt0) REVERT: c1 48 MET cc_start: 0.8172 (ttp) cc_final: 0.7742 (ttm) REVERT: c3 12 VAL cc_start: 0.8454 (t) cc_final: 0.8176 (t) REVERT: c5 6 LEU cc_start: 0.8731 (tt) cc_final: 0.8454 (tp) REVERT: c5 72 ARG cc_start: 0.6221 (tpp80) cc_final: 0.5885 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8066 (tm-30) REVERT: c8 14 LEU cc_start: 0.8838 (mt) cc_final: 0.8599 (mt) outliers start: 74 outliers final: 50 residues processed: 255 average time/residue: 0.1974 time to fit residues: 65.8667 Evaluate side-chains 271 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 56 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 173 ASN 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 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 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 30 THR Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c8 residue 68 ILE Chi-restraints excluded: chain c9 residue 6 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 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 173 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115552 restraints weight = 9185.089| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.19 r_work: 0.3435 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3666 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 : 0.753 10.044 9888 Z= 0.378 Chirality : 0.045 0.218 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.101 14.160 1043 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 10.03 % Allowed : 26.55 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 963 helix: 1.57 (0.16), residues: 897 sheet: None (None), residues: 0 loop : -1.71 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.027 0.002 PHE a 87 TYR 0.044 0.002 TYRc7 69 ARG 0.009 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 738) hydrogen bonds : angle 4.20765 ( 2214) covalent geometry : bond 0.00456 ( 7268) covalent geometry : angle 0.75347 ( 9888) *********************** 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 299 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7513 (tttm) cc_final: 0.7287 (tmtt) REVERT: a 17 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7992 (tm) REVERT: a 63 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8974 (tp) REVERT: a 90 ASN cc_start: 0.8751 (t0) cc_final: 0.8545 (t0) REVERT: a 91 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8269 (mpp) REVERT: a 210 SER cc_start: 0.9143 (t) cc_final: 0.8714 (m) REVERT: c1 32 GLU cc_start: 0.9066 (pp20) cc_final: 0.8646 (tt0) REVERT: c1 48 MET cc_start: 0.8210 (ttp) cc_final: 0.7754 (ttm) REVERT: c3 12 VAL cc_start: 0.8515 (t) cc_final: 0.8261 (t) REVERT: c5 72 ARG cc_start: 0.6233 (tpp80) cc_final: 0.5910 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8046 (tm-30) REVERT: c8 14 LEU cc_start: 0.8842 (mt) cc_final: 0.8629 (mt) outliers start: 71 outliers final: 54 residues processed: 261 average time/residue: 0.1995 time to fit residues: 68.1426 Evaluate side-chains 275 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 56 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 114 THR 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 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 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 6 LEU 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 c8 residue 68 ILE Chi-restraints excluded: chain c9 residue 6 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3952 r_free = 0.3952 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115982 restraints weight = 9257.449| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.23 r_work: 0.3444 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3807 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= 0.186 Angle : 0.766 10.141 9888 Z= 0.384 Chirality : 0.045 0.219 1266 Planarity : 0.007 0.069 1220 Dihedral : 4.110 14.895 1043 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 9.46 % Allowed : 27.54 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 963 helix: 1.59 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.69 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.017 0.002 PHE a 56 TYR 0.044 0.002 TYRc7 69 ARG 0.012 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 738) hydrogen bonds : angle 4.22327 ( 2214) covalent geometry : bond 0.00445 ( 7268) covalent geometry : angle 0.76601 ( 9888) *********************** 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 287 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7553 (tttm) cc_final: 0.7343 (tmtt) REVERT: a 17 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7960 (tm) REVERT: a 63 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8992 (tp) REVERT: a 91 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8203 (mpp) REVERT: a 210 SER cc_start: 0.9150 (t) cc_final: 0.8722 (m) REVERT: a 228 TYR cc_start: 0.8955 (m-80) cc_final: 0.8700 (m-80) REVERT: c0 69 TYR cc_start: 0.8506 (m-80) cc_final: 0.8127 (m-80) REVERT: c1 32 GLU cc_start: 0.9057 (pp20) cc_final: 0.8628 (tt0) REVERT: c1 48 MET cc_start: 0.8197 (ttp) cc_final: 0.7729 (ttm) REVERT: c3 12 VAL cc_start: 0.8524 (t) cc_final: 0.8274 (t) REVERT: c3 36 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8560 (ttm-80) REVERT: c5 72 ARG cc_start: 0.6251 (tpp80) cc_final: 0.5931 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8071 (tm-30) outliers start: 67 outliers final: 55 residues processed: 251 average time/residue: 0.1911 time to fit residues: 63.2353 Evaluate side-chains 277 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 12 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 56 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 114 THR 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 60 ILE 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 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 c5 residue 52 VAL Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c8 residue 68 ILE Chi-restraints excluded: chain c9 residue 6 LEU 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 22 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3953 r_free = 0.3953 target = 0.146974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115679 restraints weight = 9296.170| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.22 r_work: 0.3443 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3857 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= 0.185 Angle : 0.770 10.037 9888 Z= 0.385 Chirality : 0.045 0.217 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.107 14.710 1043 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 9.89 % Allowed : 27.68 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.26), residues: 963 helix: 1.60 (0.16), residues: 897 sheet: None (None), residues: 0 loop : -1.72 (0.90), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.025 0.002 PHE a 87 TYR 0.045 0.002 TYRc7 69 ARG 0.014 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 738) hydrogen bonds : angle 4.23200 ( 2214) covalent geometry : bond 0.00442 ( 7268) covalent geometry : angle 0.77032 ( 9888) *********************** 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 296 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7512 (tttm) cc_final: 0.7288 (tmtt) REVERT: a 17 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7873 (tm) REVERT: a 63 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8987 (tp) REVERT: a 91 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7890 (mpp) REVERT: a 210 SER cc_start: 0.9104 (t) cc_final: 0.8672 (m) REVERT: a 228 TYR cc_start: 0.8935 (m-80) cc_final: 0.8670 (m-80) REVERT: c0 69 TYR cc_start: 0.8450 (m-80) cc_final: 0.8066 (m-80) REVERT: c1 32 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: c1 48 MET cc_start: 0.8187 (ttp) cc_final: 0.7719 (ttm) REVERT: c3 12 VAL cc_start: 0.8519 (t) cc_final: 0.8264 (t) REVERT: c3 36 ARG cc_start: 0.8815 (ttm170) cc_final: 0.8549 (ttm-80) REVERT: c4 48 MET cc_start: 0.9227 (ttp) cc_final: 0.8952 (ttt) REVERT: c5 72 ARG cc_start: 0.6219 (tpp80) cc_final: 0.5909 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8084 (tm-30) REVERT: c7 72 ARG cc_start: 0.6181 (ttm170) cc_final: 0.5977 (ttm170) outliers start: 70 outliers final: 59 residues processed: 259 average time/residue: 0.2062 time to fit residues: 71.1487 Evaluate side-chains 284 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 12 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 56 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 114 THR 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 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 60 ILE 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 48 MET 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 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 c5 residue 52 VAL Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 48 MET Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c8 residue 68 ILE Chi-restraints excluded: chain c9 residue 6 LEU 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 57 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.147745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116279 restraints weight = 9461.426| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.26 r_work: 0.3454 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3921 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= 0.184 Angle : 0.772 9.959 9888 Z= 0.386 Chirality : 0.046 0.216 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.124 14.962 1043 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 9.32 % Allowed : 27.82 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.26), residues: 963 helix: 1.61 (0.16), residues: 896 sheet: None (None), residues: 0 loop : -1.76 (0.86), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.024 0.002 PHEc6 65 TYR 0.045 0.002 TYRc7 69 ARG 0.014 0.001 ARGc0 72 Details of bonding type rmsd hydrogen bonds : bond 0.04915 ( 738) hydrogen bonds : angle 4.24380 ( 2214) covalent geometry : bond 0.00438 ( 7268) covalent geometry : angle 0.77173 ( 9888) ********************** 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 291 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7476 (tttm) cc_final: 0.7274 (tmtt) REVERT: b1 11 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (mt) REVERT: a 17 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7845 (tm) REVERT: a 91 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: a 210 SER cc_start: 0.9086 (t) cc_final: 0.8665 (m) REVERT: a 228 TYR cc_start: 0.8951 (m-80) cc_final: 0.8714 (m-80) REVERT: c0 69 TYR cc_start: 0.8430 (m-80) cc_final: 0.8124 (m-80) REVERT: c1 32 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: c1 37 GLN cc_start: 0.7948 (pm20) cc_final: 0.7474 (pm20) REVERT: c1 48 MET cc_start: 0.8186 (ttp) cc_final: 0.7715 (ttm) REVERT: c3 12 VAL cc_start: 0.8496 (t) cc_final: 0.8242 (t) REVERT: c3 36 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8554 (ttm-80) REVERT: c5 72 ARG cc_start: 0.6218 (tpp80) cc_final: 0.5907 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8114 (tm-30) outliers start: 66 outliers final: 56 residues processed: 257 average time/residue: 0.1997 time to fit residues: 67.6035 Evaluate side-chains 281 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 12 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 56 PHE Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain a residue 127 THR 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 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 48 MET 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 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 c5 residue 52 VAL Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU 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 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 48 MET Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c8 residue 68 ILE 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: 0.6980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.147574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116386 restraints weight = 9284.678| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.32 r_work: 0.3444 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3960 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= 0.185 Angle : 0.784 11.498 9888 Z= 0.390 Chirality : 0.046 0.218 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.156 14.812 1043 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 8.33 % Allowed : 29.10 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 963 helix: 1.58 (0.16), residues: 896 sheet: None (None), residues: 0 loop : -1.79 (0.85), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.032 0.002 PHEc5 67 TYR 0.045 0.002 TYRc7 69 ARG 0.014 0.001 ARGc3 72 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 738) hydrogen bonds : angle 4.25904 ( 2214) covalent geometry : bond 0.00444 ( 7268) covalent geometry : angle 0.78353 ( 9888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.22 seconds wall clock time: 58 minutes 59.80 seconds (3539.80 seconds total)