Starting phenix.real_space_refine on Tue Feb 13 17:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_9327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_9327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_9327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_9327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/02_2024/6n2d_9327.pdb" } 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 Residue "b2 ARG 40": "NH1" <-> "NH2" Residue "b1 ARG 40": "NH1" <-> "NH2" Residue "a ARG 39": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "c0 ARG 36": "NH1" <-> "NH2" Residue "c2 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 72": "NH1" <-> "NH2" Residue "c4 ARG 36": "NH1" <-> "NH2" Residue "c5 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 36": "NH1" <-> "NH2" Residue "c7 ARG 36": "NH1" <-> "NH2" Residue "c8 ARG 29": "NH1" <-> "NH2" Residue "c8 ARG 36": "NH1" <-> "NH2" Residue "c9 ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.40, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.07 Conformation dependent library (CDL) restraints added in 2.1 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: 0.60 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: 2.35 Time building geometry restraints manager: 3.27 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: 96.11 - 103.68: 85 103.68 - 111.26: 2760 111.26 - 118.83: 3216 118.83 - 126.40: 3765 126.40 - 133.97: 62 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 2.440 nonbonded pdb=" O VALc3 63 " pdb=" OG SERc3 66 " model vdw 2.299 2.440 ... (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 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.380 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.020 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- 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= 0.490 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 262 time to evaluate : 0.811 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: 0.2288 time to fit residues: 76.8029 Evaluate side-chains 210 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7268 Z= 0.261 Angle : 0.747 10.551 9888 Z= 0.382 Chirality : 0.044 0.213 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.454 20.334 1043 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 0.09 (0.26), residues: 963 helix: 0.39 (0.16), residues: 891 sheet: None (None), residues: 0 loop : -2.77 (0.67), residues: 72 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 0.021 0.002 PHE a 87 TYR 0.042 0.002 TYRc6 69 ARG 0.008 0.001 ARGc0 72 *********************** 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 284 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 227 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: b2 36 ILE cc_start: 0.8028 (tt) cc_final: 0.7767 (tt) REVERT: b1 17 MET cc_start: 0.8707 (mmm) cc_final: 0.8254 (mmm) REVERT: a 17 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8237 (tm) REVERT: a 203 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7893 (tmm) REVERT: a 210 SER cc_start: 0.9118 (t) cc_final: 0.8612 (m) REVERT: c3 12 VAL cc_start: 0.8571 (t) cc_final: 0.8304 (t) REVERT: c5 6 LEU cc_start: 0.8653 (tt) cc_final: 0.8421 (tp) REVERT: c5 67 PHE cc_start: 0.8568 (m-80) cc_final: 0.7746 (m-80) REVERT: c5 72 ARG cc_start: 0.5971 (tpp80) cc_final: 0.5655 (tpp-160) REVERT: c6 32 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7356 (tm-30) REVERT: c6 37 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8191 (tm-30) REVERT: c7 30 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8751 (m) outliers start: 57 outliers final: 30 residues processed: 257 average time/residue: 0.2024 time to fit residues: 67.3366 Evaluate side-chains 237 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 160 PHE 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 61 ILE Chi-restraints excluded: chain c2 residue 68 ILE Chi-restraints excluded: chain c3 residue 66 SER 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 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 67 PHE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 70 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 99 HIS a 207 GLN ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2896 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= 0.281 Angle : 0.744 10.248 9888 Z= 0.374 Chirality : 0.045 0.219 1266 Planarity : 0.007 0.062 1220 Dihedral : 4.275 18.240 1043 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 9.04 % Allowed : 23.59 % Favored : 67.37 % 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: 1.19 (0.26), residues: 963 helix: 1.09 (0.17), residues: 892 sheet: None (None), residues: 0 loop : -2.34 (0.74), residues: 71 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 0.023 0.002 PHE a 87 TYR 0.028 0.002 TYRc6 69 ARG 0.008 0.001 ARGc6 72 *********************** 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 286 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 222 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: b2 36 ILE cc_start: 0.8035 (tt) cc_final: 0.7821 (tt) REVERT: a 17 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (tm) REVERT: a 63 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8907 (tp) REVERT: a 105 TRP cc_start: 0.7682 (m100) cc_final: 0.7318 (m100) REVERT: a 207 GLN cc_start: 0.8967 (tt0) cc_final: 0.8708 (tt0) REVERT: a 210 SER cc_start: 0.9158 (t) cc_final: 0.8800 (m) REVERT: c1 32 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: c2 54 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8953 (mp) REVERT: c3 12 VAL cc_start: 0.8495 (t) cc_final: 0.8211 (t) REVERT: c5 6 LEU cc_start: 0.8675 (tt) cc_final: 0.8434 (tp) REVERT: c5 72 ARG cc_start: 0.6183 (tpp80) cc_final: 0.5824 (tpp-160) REVERT: c6 29 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8458 (mmm-85) REVERT: c6 32 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7512 (tm-30) REVERT: c6 48 MET cc_start: 0.8258 (ttp) cc_final: 0.8040 (ttp) REVERT: c7 72 ARG cc_start: 0.6226 (ttm170) cc_final: 0.5955 (ttm170) REVERT: c8 14 LEU cc_start: 0.8771 (mt) cc_final: 0.8550 (mt) outliers start: 64 outliers final: 34 residues processed: 257 average time/residue: 0.2015 time to fit residues: 67.4453 Evaluate side-chains 251 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 65 SER Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 54 LEU Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** c2 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3191 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= 0.288 Angle : 0.744 10.593 9888 Z= 0.373 Chirality : 0.045 0.214 1266 Planarity : 0.007 0.063 1220 Dihedral : 4.159 15.271 1043 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 9.32 % Allowed : 24.72 % Favored : 65.96 % 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: 1.66 (0.27), residues: 963 helix: 1.38 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.24 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPb2 30 HIS 0.008 0.002 HIS a 99 PHE 0.020 0.002 PHE a 56 TYR 0.023 0.002 TYRc6 69 ARG 0.008 0.001 ARGc6 72 *********************** 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 291 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: b2 36 ILE cc_start: 0.7986 (tt) cc_final: 0.7777 (tt) REVERT: a 17 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8071 (tm) REVERT: a 56 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: a 105 TRP cc_start: 0.7771 (m100) cc_final: 0.7435 (m100) REVERT: a 210 SER cc_start: 0.9159 (t) cc_final: 0.8769 (m) REVERT: c1 32 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: c3 12 VAL cc_start: 0.8507 (t) cc_final: 0.8221 (t) REVERT: c5 72 ARG cc_start: 0.6177 (tpp80) cc_final: 0.5779 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7570 (tm-30) REVERT: c6 48 MET cc_start: 0.8335 (ttp) cc_final: 0.8117 (ttp) REVERT: c7 72 ARG cc_start: 0.6134 (ttm170) cc_final: 0.5891 (ttm170) REVERT: c8 40 LEU cc_start: 0.8435 (mp) cc_final: 0.8184 (mt) REVERT: c9 30 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8833 (m) outliers start: 66 outliers final: 42 residues processed: 260 average time/residue: 0.1924 time to fit residues: 65.6278 Evaluate side-chains 261 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 65 SER Chi-restraints excluded: chain a residue 110 THR 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 c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c5 residue 68 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 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 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 78 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3400 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= 0.262 Angle : 0.730 10.215 9888 Z= 0.365 Chirality : 0.044 0.211 1266 Planarity : 0.006 0.065 1220 Dihedral : 4.104 14.808 1043 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 9.18 % Allowed : 25.42 % Favored : 65.40 % 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: 1.95 (0.27), residues: 963 helix: 1.57 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.20 (0.84), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 206 HIS 0.005 0.001 HIS a 128 PHE 0.027 0.002 PHE a 87 TYR 0.022 0.002 TYR a 175 ARG 0.010 0.001 ARGc6 72 *********************** 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 291 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 226 time to evaluate : 0.792 Fit side-chains REVERT: b2 27 LYS cc_start: 0.7636 (tttm) cc_final: 0.7336 (tmtt) REVERT: a 17 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (tm) REVERT: a 63 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8948 (tp) REVERT: a 210 SER cc_start: 0.9153 (t) cc_final: 0.8780 (m) REVERT: c0 69 TYR cc_start: 0.8342 (m-80) cc_final: 0.8083 (m-80) REVERT: c1 32 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: c1 48 MET cc_start: 0.7892 (ttp) cc_final: 0.7491 (ttm) REVERT: c3 12 VAL cc_start: 0.8472 (t) cc_final: 0.8158 (t) REVERT: c4 31 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8466 (tt) REVERT: c5 72 ARG cc_start: 0.6179 (tpp80) cc_final: 0.5836 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7630 (tm-30) REVERT: c7 72 ARG cc_start: 0.6037 (ttm170) cc_final: 0.5814 (ttm170) REVERT: c9 30 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8802 (m) outliers start: 65 outliers final: 41 residues processed: 260 average time/residue: 0.2023 time to fit residues: 68.0765 Evaluate side-chains 266 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain a residue 99 HIS Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain 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 c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain 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 31 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7268 Z= 0.290 Angle : 0.748 10.455 9888 Z= 0.375 Chirality : 0.045 0.210 1266 Planarity : 0.007 0.065 1220 Dihedral : 4.126 19.002 1043 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 10.59 % Allowed : 25.42 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.26), residues: 963 helix: 1.59 (0.17), residues: 895 sheet: None (None), residues: 0 loop : -1.98 (0.84), residues: 68 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 0.019 0.002 PHE a 56 TYR 0.019 0.002 TYR a 228 ARG 0.011 0.001 ARGc0 72 *********************** 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 297 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 222 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7666 (tttm) cc_final: 0.7374 (tmtt) REVERT: a 17 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8067 (tm) REVERT: a 63 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8983 (tp) REVERT: a 91 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7377 (mpp) REVERT: a 210 SER cc_start: 0.9161 (t) cc_final: 0.8798 (m) REVERT: c1 32 GLU cc_start: 0.8907 (pp20) cc_final: 0.8469 (tt0) REVERT: c1 48 MET cc_start: 0.7995 (ttp) cc_final: 0.7578 (ttm) REVERT: c3 12 VAL cc_start: 0.8543 (t) cc_final: 0.8258 (t) REVERT: c4 31 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (tt) REVERT: c4 41 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7370 (tmm-80) REVERT: c5 72 ARG cc_start: 0.6211 (tpp80) cc_final: 0.5855 (tpp-160) REVERT: c6 29 ARG cc_start: 0.8898 (mtt-85) cc_final: 0.8448 (mtp180) REVERT: c6 32 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7658 (tm-30) REVERT: c7 72 ARG cc_start: 0.6120 (ttm170) cc_final: 0.5907 (ttm170) REVERT: c8 14 LEU cc_start: 0.8805 (mt) cc_final: 0.8575 (mt) REVERT: c9 30 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8816 (m) outliers start: 75 outliers final: 48 residues processed: 260 average time/residue: 0.1995 time to fit residues: 67.9220 Evaluate side-chains 272 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 218 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU 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 65 SER 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 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 63 VAL Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c3 residue 68 ILE Chi-restraints excluded: chain c4 residue 31 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 41 ARG Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 52 VAL Chi-restraints excluded: chain c5 residue 68 ILE Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 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 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3727 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= 0.254 Angle : 0.741 9.637 9888 Z= 0.369 Chirality : 0.044 0.222 1266 Planarity : 0.007 0.066 1220 Dihedral : 4.119 16.842 1043 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 9.46 % Allowed : 26.55 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.19 (0.26), residues: 963 helix: 1.73 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -2.00 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.026 0.001 PHE a 87 TYR 0.025 0.001 TYR a 175 ARG 0.012 0.001 ARGc6 72 *********************** 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 291 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7609 (tttm) cc_final: 0.7370 (tmtt) REVERT: a 17 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7917 (tm) REVERT: a 63 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8973 (tp) REVERT: a 207 GLN cc_start: 0.9026 (tt0) cc_final: 0.8657 (tt0) REVERT: a 210 SER cc_start: 0.9163 (t) cc_final: 0.8771 (m) REVERT: c0 69 TYR cc_start: 0.8417 (m-80) cc_final: 0.8037 (m-80) REVERT: c1 32 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: c1 48 MET cc_start: 0.7929 (ttp) cc_final: 0.7459 (ttm) REVERT: c2 32 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8521 (tt0) REVERT: c3 12 VAL cc_start: 0.8414 (t) cc_final: 0.8078 (t) REVERT: c4 41 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7380 (tmm-80) REVERT: c5 72 ARG cc_start: 0.6240 (tpp80) cc_final: 0.5911 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7653 (tm-30) REVERT: c6 72 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7435 (ttm170) REVERT: c7 72 ARG cc_start: 0.5969 (ttm170) cc_final: 0.5734 (ttm170) REVERT: c8 14 LEU cc_start: 0.8818 (mt) cc_final: 0.8592 (mt) REVERT: c9 30 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8784 (m) outliers start: 67 outliers final: 46 residues processed: 259 average time/residue: 0.2076 time to fit residues: 69.8648 Evaluate side-chains 266 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 215 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain 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 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 41 ARG 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 c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 58 LEU Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0070 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c4 45 GLN ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7268 Z= 0.250 Angle : 0.739 9.065 9888 Z= 0.367 Chirality : 0.044 0.226 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.104 15.094 1043 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 8.19 % Allowed : 27.54 % Favored : 64.27 % 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: 2.26 (0.26), residues: 963 helix: 1.78 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.10 (0.82), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.018 0.002 PHEc6 65 TYR 0.043 0.002 TYRc7 69 ARG 0.012 0.001 ARGc0 72 *********************** 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 278 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 220 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7508 (tttm) cc_final: 0.7267 (tmtt) REVERT: a 17 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7878 (tm) REVERT: a 91 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7580 (mpp) REVERT: a 207 GLN cc_start: 0.9026 (tt0) cc_final: 0.8696 (tt0) REVERT: a 210 SER cc_start: 0.9166 (t) cc_final: 0.8772 (m) REVERT: c0 69 TYR cc_start: 0.8381 (m-80) cc_final: 0.8079 (m-80) REVERT: c1 32 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: c1 48 MET cc_start: 0.7844 (ttp) cc_final: 0.7420 (ttm) REVERT: c2 32 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8545 (tt0) REVERT: c2 48 MET cc_start: 0.8945 (ttp) cc_final: 0.8699 (ttt) REVERT: c3 12 VAL cc_start: 0.8423 (t) cc_final: 0.8090 (t) REVERT: c4 41 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7355 (tmm-80) REVERT: c5 72 ARG cc_start: 0.6182 (tpp80) cc_final: 0.5901 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7725 (tm-30) REVERT: c6 72 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7488 (ttm170) REVERT: c8 14 LEU cc_start: 0.8799 (mt) cc_final: 0.8587 (mt) REVERT: c9 30 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8772 (m) outliers start: 58 outliers final: 43 residues processed: 249 average time/residue: 0.2109 time to fit residues: 68.1945 Evaluate side-chains 258 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 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 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 66 SER Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c0 residue 70 LEU Chi-restraints excluded: chain c1 residue 6 LEU Chi-restraints excluded: chain c1 residue 32 GLU Chi-restraints excluded: chain c1 residue 34 ILE Chi-restraints excluded: chain c1 residue 54 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c3 residue 52 VAL Chi-restraints excluded: chain c3 residue 66 SER Chi-restraints excluded: chain c3 residue 67 PHE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 41 ARG Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 63 VAL Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7268 Z= 0.277 Angle : 0.754 9.376 9888 Z= 0.377 Chirality : 0.045 0.225 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.113 18.180 1043 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 8.19 % Allowed : 27.97 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.26), residues: 963 helix: 1.75 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.93 (0.82), residues: 69 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 0.018 0.001 PHE a 87 TYR 0.043 0.002 TYRc7 69 ARG 0.014 0.001 ARGc0 72 *********************** 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 279 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7546 (tttm) cc_final: 0.7285 (tmtt) REVERT: a 17 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7903 (tm) REVERT: a 91 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7797 (mpp) REVERT: a 210 SER cc_start: 0.9186 (t) cc_final: 0.8792 (m) REVERT: c0 69 TYR cc_start: 0.8390 (m-80) cc_final: 0.8102 (m-80) REVERT: c1 32 GLU cc_start: 0.8876 (pp20) cc_final: 0.8519 (tt0) REVERT: c1 48 MET cc_start: 0.7871 (ttp) cc_final: 0.7446 (ttm) REVERT: c3 12 VAL cc_start: 0.8460 (t) cc_final: 0.8136 (t) REVERT: c4 41 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7340 (tmm-80) REVERT: c5 72 ARG cc_start: 0.6259 (tpp80) cc_final: 0.5930 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7705 (tm-30) REVERT: c6 56 GLU cc_start: 0.7742 (tt0) cc_final: 0.7431 (tt0) REVERT: c6 72 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7495 (ttm170) REVERT: c8 14 LEU cc_start: 0.8800 (mt) cc_final: 0.8575 (mt) outliers start: 58 outliers final: 46 residues processed: 248 average time/residue: 0.2193 time to fit residues: 69.9245 Evaluate side-chains 265 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 65 SER Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 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 41 ARG 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 c6 residue 34 ILE 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 48 MET Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7268 Z= 0.310 Angle : 0.787 11.872 9888 Z= 0.393 Chirality : 0.046 0.226 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.137 17.762 1043 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 7.77 % Allowed : 29.52 % Favored : 62.71 % 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: 2.08 (0.26), residues: 963 helix: 1.65 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.85 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.020 0.002 PHE a 87 TYR 0.049 0.002 TYRc7 69 ARG 0.014 0.001 ARGc0 72 ********************** 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 274 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 219 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.7535 (tttm) cc_final: 0.7261 (tmtt) REVERT: a 17 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8026 (tm) REVERT: a 210 SER cc_start: 0.9185 (t) cc_final: 0.8796 (m) REVERT: c0 69 TYR cc_start: 0.8459 (m-80) cc_final: 0.8194 (m-80) REVERT: c1 32 GLU cc_start: 0.8908 (pp20) cc_final: 0.8506 (tt0) REVERT: c1 48 MET cc_start: 0.7964 (ttp) cc_final: 0.7547 (ttm) REVERT: c1 67 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: c3 12 VAL cc_start: 0.8549 (t) cc_final: 0.8269 (t) REVERT: c4 41 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7395 (tmm-80) REVERT: c5 72 ARG cc_start: 0.6261 (tpp80) cc_final: 0.5930 (tpp-160) REVERT: c6 32 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 55 outliers final: 50 residues processed: 246 average time/residue: 0.2069 time to fit residues: 66.0996 Evaluate side-chains 270 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 65 SER Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 220 ILE Chi-restraints excluded: chain c0 residue 28 SER Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 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 c1 residue 67 PHE 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 41 ARG Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c4 residue 68 ILE Chi-restraints excluded: chain c5 residue 5 VAL Chi-restraints excluded: chain c5 residue 29 ARG Chi-restraints excluded: chain c6 residue 34 ILE Chi-restraints excluded: chain c6 residue 67 PHE Chi-restraints excluded: chain c7 residue 21 ILE Chi-restraints excluded: chain c7 residue 26 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 34 ILE Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c7 residue 52 VAL Chi-restraints excluded: chain c8 residue 34 ILE Chi-restraints excluded: chain c8 residue 48 MET Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 12 VAL Chi-restraints excluded: chain c9 residue 30 THR Chi-restraints excluded: chain c9 residue 34 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 63 VAL Chi-restraints excluded: chain c9 residue 66 SER Chi-restraints excluded: chain c9 residue 67 PHE Chi-restraints excluded: chain c9 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117865 restraints weight = 8943.114| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.07 r_work: 0.3469 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7268 Z= 0.295 Angle : 0.783 11.168 9888 Z= 0.391 Chirality : 0.046 0.224 1266 Planarity : 0.007 0.067 1220 Dihedral : 4.166 17.847 1043 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 8.76 % Allowed : 28.81 % 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: 2.07 (0.26), residues: 963 helix: 1.64 (0.16), residues: 894 sheet: None (None), residues: 0 loop : -1.83 (0.79), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 206 HIS 0.004 0.001 HIS a 128 PHE 0.029 0.002 PHEc5 67 TYR 0.048 0.002 TYRc7 69 ARG 0.014 0.001 ARGc3 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.54 seconds wall clock time: 38 minutes 5.90 seconds (2285.90 seconds total)