Starting phenix.real_space_refine on Wed Aug 5 07:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.cif Found real_map, /net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21en_67612/08_2026/21en_67612.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5430 2.51 5 N 1488 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "D" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "F" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8691 At special positions: 0 Unit cell: (139.872, 136.112, 87.984, 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 48 16.00 O 1725 8.00 N 1488 7.00 C 5430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.01 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.01 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.01 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 500.7 milliseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 7.3% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.919A pdb=" N TYR A 33 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.521A pdb=" N THR A 92 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.513A pdb=" N LEU A 208 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.924A pdb=" N TYR B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.506A pdb=" N THR B 92 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.907A pdb=" N TYR C 33 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'D' and resid 131 through 136 removed outlier: 3.573A pdb=" N THR D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.600A pdb=" N THR E 135 " --> pdb=" O ASN E 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.655A pdb=" N THR F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.553A pdb=" N MET A 35 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 51 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.795A pdb=" N VAL A 114 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.498A pdb=" N VAL A 158 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 174 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP A 160 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 138 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.577A pdb=" N MET B 35 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP B 37 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.793A pdb=" N VAL B 114 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.485A pdb=" N VAL B 158 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR B 174 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP B 160 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 135 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.569A pdb=" N MET C 35 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.775A pdb=" N VAL C 114 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AB8, first strand: chain 'C' and resid 135 through 138 removed outlier: 6.523A pdb=" N VAL C 158 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR C 174 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP C 160 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 135 through 138 Processing sheet with id=AC1, first strand: chain 'D' and resid 94 through 101 Processing sheet with id=AC2, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.313A pdb=" N ASP D 83 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 47 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 85 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY D 44 " --> pdb=" O HIS D 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 94 through 101 Processing sheet with id=AC4, first strand: chain 'E' and resid 83 through 89 removed outlier: 5.315A pdb=" N ASP E 83 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL E 47 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY E 85 " --> pdb=" O PHE E 45 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY E 44 " --> pdb=" O HIS E 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 94 through 101 Processing sheet with id=AC6, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.303A pdb=" N ASP F 83 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL F 47 " --> pdb=" O ASP F 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 85 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY F 44 " --> pdb=" O HIS F 120 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1658 1.31 - 1.44: 2295 1.44 - 1.56: 4846 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8871 Sorted by residual: bond pdb=" CA SER D 107 " pdb=" CB SER D 107 " ideal model delta sigma weight residual 1.533 1.422 0.111 1.66e-02 3.63e+03 4.46e+01 bond pdb=" CA SER C 125 " pdb=" CB SER C 125 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.45e-02 4.76e+03 2.19e+01 bond pdb=" C ILE C 127 " pdb=" O ILE C 127 " ideal model delta sigma weight residual 1.236 1.201 0.035 9.80e-03 1.04e+04 1.27e+01 bond pdb=" CB ASN C 53 " pdb=" CG ASN C 53 " ideal model delta sigma weight residual 1.516 1.432 0.084 2.50e-02 1.60e+03 1.13e+01 bond pdb=" CB ASN A 53 " pdb=" CG ASN A 53 " ideal model delta sigma weight residual 1.516 1.432 0.084 2.50e-02 1.60e+03 1.12e+01 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 11365 2.44 - 4.88: 534 4.88 - 7.32: 80 7.32 - 9.76: 16 9.76 - 12.20: 5 Bond angle restraints: 12000 Sorted by residual: angle pdb=" O VAL C 123 " pdb=" C VAL C 123 " pdb=" N SER C 124 " ideal model delta sigma weight residual 123.10 131.78 -8.68 1.17e+00 7.31e-01 5.51e+01 angle pdb=" CA VAL C 123 " pdb=" C VAL C 123 " pdb=" N SER C 124 " ideal model delta sigma weight residual 116.34 107.18 9.16 1.28e+00 6.10e-01 5.12e+01 angle pdb=" N SER C 124 " pdb=" CA SER C 124 " pdb=" C SER C 124 " ideal model delta sigma weight residual 110.41 118.54 -8.13 1.23e+00 6.61e-01 4.37e+01 angle pdb=" C GLU E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 122.32 114.49 7.83 1.76e+00 3.23e-01 1.98e+01 angle pdb=" C GLU D 51 " pdb=" N ASP D 52 " pdb=" CA ASP D 52 " ideal model delta sigma weight residual 122.32 114.52 7.80 1.76e+00 3.23e-01 1.96e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4932 17.72 - 35.45: 191 35.45 - 53.17: 80 53.17 - 70.89: 23 70.89 - 88.62: 3 Dihedral angle restraints: 5229 sinusoidal: 2019 harmonic: 3210 Sorted by residual: dihedral pdb=" CD ARG A 143 " pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " pdb=" NH1 ARG A 143 " ideal model delta sinusoidal sigma weight residual 0.00 52.58 -52.58 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA LEU C 73 " pdb=" C LEU C 73 " pdb=" N GLU C 74 " pdb=" CA GLU C 74 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU A 73 " pdb=" C LEU A 73 " pdb=" N GLU A 74 " pdb=" CA GLU A 74 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 730 0.056 - 0.111: 366 0.111 - 0.167: 164 0.167 - 0.222: 41 0.222 - 0.278: 7 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB VAL B 38 " pdb=" CA VAL B 38 " pdb=" CG1 VAL B 38 " pdb=" CG2 VAL B 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL C 38 " pdb=" CA VAL C 38 " pdb=" CG1 VAL C 38 " pdb=" CG2 VAL C 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL A 38 " pdb=" CA VAL A 38 " pdb=" CG1 VAL A 38 " pdb=" CG2 VAL A 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1305 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 143 " -0.879 9.50e-02 1.11e+02 3.94e-01 9.42e+01 pdb=" NE ARG A 143 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 143 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 143 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 143 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 123 " 0.017 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C VAL C 123 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL C 123 " 0.028 2.00e-02 2.50e+03 pdb=" N SER C 124 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 34 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C GLY B 34 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B 34 " 0.020 2.00e-02 2.50e+03 pdb=" N MET B 35 " 0.018 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1175 2.74 - 3.28: 7734 3.28 - 3.82: 14328 3.82 - 4.36: 18367 4.36 - 4.90: 31558 Nonbonded interactions: 73162 Sorted by model distance: nonbonded pdb=" OG1 THR B 102 " pdb=" OD2 ASP B 113 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 139 " pdb=" NZ LYS C 232 " model vdw 2.222 3.120 nonbonded pdb=" NE2 HIS D 46 " pdb=" OD2 ASP D 124 " model vdw 2.294 3.120 nonbonded pdb=" NE2 HIS F 46 " pdb=" OD2 ASP F 124 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG E 79 " pdb=" O ASP E 83 " model vdw 2.300 3.120 ... (remaining 73157 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 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 : 0.020 0.145 8877 Z= 0.819 Angle : 1.230 12.203 12012 Z= 0.674 Chirality : 0.078 0.278 1308 Planarity : 0.013 0.394 1572 Dihedral : 12.199 88.618 3195 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.79 % Allowed : 4.46 % Favored : 94.75 % Rotamer: Outliers : 0.85 % Allowed : 3.61 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1143 helix: -5.36 (0.14), residues: 18 sheet: -0.82 (0.21), residues: 486 loop : -0.98 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG A 105 TYR 0.037 0.006 TYR A 55 PHE 0.044 0.005 PHE C 223 TRP 0.023 0.007 TRP C 37 HIS 0.013 0.003 HIS D 20 Details of bonding type rmsd/Z covalent geometry : bond 0.01951 / 0.82 ( 8871) covalent geometry : angle 1.22381 / 0.67 (12000) SS BOND : bond 0.01470 / 0.87 ( 6) SS BOND : angle 3.96713 / 2.24 ( 12) hydrogen bonds : bond 0.12734 / 8.91 ( 333) hydrogen bonds : angle 7.46542 / 5.19 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.7902 (mt0) cc_final: 0.7596 (mt0) REVERT: A 12 LEU cc_start: 0.7648 (tp) cc_final: 0.7413 (tm) REVERT: A 24 LYS cc_start: 0.7247 (tttt) cc_final: 0.6783 (ttmm) REVERT: A 44 LYS cc_start: 0.6643 (mmtt) cc_final: 0.5972 (ttpt) REVERT: A 47 LYS cc_start: 0.6591 (tttt) cc_final: 0.5774 (mttp) REVERT: A 64 ASP cc_start: 0.8130 (m-30) cc_final: 0.7777 (m-30) REVERT: A 88 LYS cc_start: 0.7378 (mttt) cc_final: 0.7176 (mttm) REVERT: A 130 THR cc_start: 0.8082 (m) cc_final: 0.7715 (p) REVERT: A 134 LYS cc_start: 0.7840 (mttt) cc_final: 0.7481 (tptp) REVERT: B 4 GLN cc_start: 0.7849 (mt0) cc_final: 0.7614 (mt0) REVERT: B 12 LEU cc_start: 0.7542 (tp) cc_final: 0.7308 (tm) REVERT: B 24 LYS cc_start: 0.7218 (tttt) cc_final: 0.6742 (tttm) REVERT: B 44 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6101 (ttpt) REVERT: B 47 LYS cc_start: 0.6666 (tttt) cc_final: 0.5830 (mmtm) REVERT: B 64 ASP cc_start: 0.8017 (m-30) cc_final: 0.7656 (m-30) REVERT: B 130 THR cc_start: 0.8138 (m) cc_final: 0.7746 (p) REVERT: B 167 GLN cc_start: 0.7576 (mt0) cc_final: 0.7369 (mt0) REVERT: B 194 THR cc_start: 0.8254 (p) cc_final: 0.8001 (p) REVERT: C 4 GLN cc_start: 0.7787 (mt0) cc_final: 0.7561 (mt0) REVERT: C 24 LYS cc_start: 0.7285 (tttt) cc_final: 0.6762 (ttmt) REVERT: C 44 LYS cc_start: 0.6652 (mmtt) cc_final: 0.5950 (ttpt) REVERT: C 47 LYS cc_start: 0.6481 (tttt) cc_final: 0.5646 (mttp) REVERT: C 64 ASP cc_start: 0.8086 (m-30) cc_final: 0.7798 (m-30) REVERT: C 90 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: C 91 ASP cc_start: 0.7681 (m-30) cc_final: 0.7400 (m-30) REVERT: C 130 THR cc_start: 0.8171 (m) cc_final: 0.7826 (p) REVERT: C 134 LYS cc_start: 0.7960 (mttt) cc_final: 0.7647 (tptp) REVERT: C 167 GLN cc_start: 0.7658 (mt0) cc_final: 0.7417 (mt0) REVERT: C 228 LYS cc_start: 0.7648 (tttt) cc_final: 0.7069 (tttt) REVERT: D 2 GLU cc_start: 0.7859 (tt0) cc_final: 0.7077 (tt0) REVERT: D 4 LYS cc_start: 0.8293 (mttt) cc_final: 0.7840 (mtpp) REVERT: E 2 GLU cc_start: 0.7846 (tt0) cc_final: 0.7339 (pp20) REVERT: E 4 LYS cc_start: 0.8395 (mttt) cc_final: 0.7966 (mtpp) REVERT: F 2 GLU cc_start: 0.7817 (tt0) cc_final: 0.7300 (pp20) REVERT: F 4 LYS cc_start: 0.8233 (mttt) cc_final: 0.7838 (mttp) outliers start: 8 outliers final: 0 residues processed: 169 average time/residue: 0.6815 time to fit residues: 121.6067 Evaluate side-chains 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN C 153 ASN E 86 ASN F 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.196776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122814 restraints weight = 9589.788| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.81 r_work: 0.2825 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8877 Z= 0.141 Angle : 0.580 7.879 12012 Z= 0.314 Chirality : 0.047 0.138 1308 Planarity : 0.004 0.034 1572 Dihedral : 5.398 37.322 1227 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.36 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 8.28 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1143 helix: -5.31 (0.16), residues: 18 sheet: -0.56 (0.21), residues: 501 loop : -0.37 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 79 TYR 0.013 0.002 TYR B 108 PHE 0.011 0.002 PHE E 45 TRP 0.012 0.002 TRP B 48 HIS 0.001 0.000 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8871) covalent geometry : angle 0.57881 / 0.31 (12000) SS BOND : bond 0.00438 / 0.21 ( 6) SS BOND : angle 1.29858 / 0.74 ( 12) hydrogen bonds : bond 0.03491 / 2.21 ( 333) hydrogen bonds : angle 5.83461 / 4.02 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7551 (t0) cc_final: 0.7127 (m-30) REVERT: A 24 LYS cc_start: 0.8155 (tttt) cc_final: 0.7689 (ttmt) REVERT: A 44 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6357 (ttpt) REVERT: A 47 LYS cc_start: 0.8361 (tttt) cc_final: 0.7903 (mttp) REVERT: A 58 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: A 130 THR cc_start: 0.8517 (m) cc_final: 0.8036 (p) REVERT: A 134 LYS cc_start: 0.7944 (mttt) cc_final: 0.7469 (tptp) REVERT: A 149 LYS cc_start: 0.8007 (tttt) cc_final: 0.7723 (mtpt) REVERT: B 1 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.5007 (mtp) REVERT: B 24 LYS cc_start: 0.8121 (tttt) cc_final: 0.7646 (tttt) REVERT: B 44 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6421 (ttpt) REVERT: B 47 LYS cc_start: 0.8311 (tttt) cc_final: 0.7833 (mttp) REVERT: B 58 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: B 130 THR cc_start: 0.8543 (m) cc_final: 0.8089 (p) REVERT: B 149 LYS cc_start: 0.8045 (tttt) cc_final: 0.7773 (mtpt) REVERT: B 228 LYS cc_start: 0.7562 (tttt) cc_final: 0.7108 (tttt) REVERT: C 24 LYS cc_start: 0.8186 (tttt) cc_final: 0.7722 (ttmt) REVERT: C 44 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6235 (ttpt) REVERT: C 47 LYS cc_start: 0.8218 (tttt) cc_final: 0.7760 (mmtp) REVERT: C 58 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: C 74 GLU cc_start: 0.7543 (tt0) cc_final: 0.7040 (tp30) REVERT: C 130 THR cc_start: 0.8598 (m) cc_final: 0.8133 (p) REVERT: C 134 LYS cc_start: 0.8004 (mttt) cc_final: 0.7480 (tptp) REVERT: C 149 LYS cc_start: 0.8059 (tttt) cc_final: 0.7741 (mtpt) REVERT: C 228 LYS cc_start: 0.7737 (tttt) cc_final: 0.7180 (tttt) REVERT: D 1 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7585 (ttm) REVERT: D 2 GLU cc_start: 0.8400 (tt0) cc_final: 0.7581 (tt0) REVERT: D 4 LYS cc_start: 0.8137 (mttt) cc_final: 0.7799 (mtpp) REVERT: D 40 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5658 (pm20) REVERT: D 42 GLU cc_start: 0.6322 (mt-10) cc_final: 0.5997 (tp30) REVERT: E 2 GLU cc_start: 0.8376 (tt0) cc_final: 0.7691 (tm-30) REVERT: E 4 LYS cc_start: 0.8316 (mttt) cc_final: 0.7700 (mttp) REVERT: F 2 GLU cc_start: 0.8357 (tt0) cc_final: 0.7581 (tm-30) REVERT: F 4 LYS cc_start: 0.8272 (mttt) cc_final: 0.7686 (mttp) REVERT: F 42 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6149 (tp30) REVERT: F 132 GLU cc_start: 0.7598 (mp0) cc_final: 0.7102 (tm-30) REVERT: F 133 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7250 (mm-30) outliers start: 21 outliers final: 7 residues processed: 149 average time/residue: 0.7757 time to fit residues: 121.3092 Evaluate side-chains 139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.193373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121401 restraints weight = 9459.989| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.63 r_work: 0.2819 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8877 Z= 0.241 Angle : 0.597 6.716 12012 Z= 0.321 Chirality : 0.048 0.143 1308 Planarity : 0.004 0.035 1572 Dihedral : 5.027 25.207 1224 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.54 % Favored : 97.29 % Rotamer: Outliers : 3.29 % Allowed : 9.13 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1143 helix: -5.17 (0.20), residues: 18 sheet: -0.36 (0.21), residues: 489 loop : -0.37 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 79 TYR 0.015 0.002 TYR B 216 PHE 0.013 0.002 PHE B 223 TRP 0.013 0.003 TRP B 48 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 8871) covalent geometry : angle 0.59569 / 0.32 (12000) SS BOND : bond 0.00633 / 0.34 ( 6) SS BOND : angle 1.42808 / 0.82 ( 12) hydrogen bonds : bond 0.03681 / 2.38 ( 333) hydrogen bonds : angle 5.75796 / 3.96 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7715 (t0) cc_final: 0.7204 (m-30) REVERT: A 24 LYS cc_start: 0.8188 (tttt) cc_final: 0.7687 (ttmt) REVERT: A 44 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6416 (ttpt) REVERT: A 47 LYS cc_start: 0.8324 (tttt) cc_final: 0.7783 (mttp) REVERT: A 58 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 90 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: A 130 THR cc_start: 0.8453 (m) cc_final: 0.8050 (p) REVERT: A 134 LYS cc_start: 0.7952 (mttt) cc_final: 0.7390 (tptp) REVERT: A 149 LYS cc_start: 0.7996 (tttt) cc_final: 0.7751 (mtpt) REVERT: B 1 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5190 (mtp) REVERT: B 44 LYS cc_start: 0.7076 (mmtt) cc_final: 0.6463 (ttpt) REVERT: B 47 LYS cc_start: 0.8304 (tttt) cc_final: 0.7752 (mttp) REVERT: B 58 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: B 74 GLU cc_start: 0.7505 (tt0) cc_final: 0.6903 (tp30) REVERT: B 130 THR cc_start: 0.8524 (m) cc_final: 0.8124 (p) REVERT: B 133 GLN cc_start: 0.7595 (mt0) cc_final: 0.7204 (pm20) REVERT: B 149 LYS cc_start: 0.8032 (tttt) cc_final: 0.7747 (mtpt) REVERT: B 167 GLN cc_start: 0.8113 (mt0) cc_final: 0.7758 (mt0) REVERT: B 228 LYS cc_start: 0.7554 (tttt) cc_final: 0.7131 (tttp) REVERT: C 24 LYS cc_start: 0.8224 (tttt) cc_final: 0.7817 (tttm) REVERT: C 44 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6286 (ttpt) REVERT: C 47 LYS cc_start: 0.8201 (tttt) cc_final: 0.7694 (mttp) REVERT: C 58 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: C 74 GLU cc_start: 0.7404 (tt0) cc_final: 0.6845 (tp30) REVERT: C 134 LYS cc_start: 0.7984 (mttt) cc_final: 0.7543 (tptp) REVERT: C 228 LYS cc_start: 0.7743 (tttt) cc_final: 0.7260 (tttt) REVERT: D 2 GLU cc_start: 0.8403 (tt0) cc_final: 0.7576 (tt0) REVERT: D 4 LYS cc_start: 0.8168 (mttt) cc_final: 0.7797 (mtpp) REVERT: D 40 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5668 (pm20) REVERT: D 42 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5957 (tp30) REVERT: D 51 GLU cc_start: 0.6526 (tt0) cc_final: 0.5965 (tp30) REVERT: E 2 GLU cc_start: 0.8395 (tt0) cc_final: 0.7651 (tm-30) REVERT: E 4 LYS cc_start: 0.8286 (mttt) cc_final: 0.7708 (mtpp) REVERT: F 2 GLU cc_start: 0.8399 (tt0) cc_final: 0.7592 (tm-30) REVERT: F 4 LYS cc_start: 0.8246 (mttt) cc_final: 0.7694 (mttp) REVERT: F 132 GLU cc_start: 0.7639 (mp0) cc_final: 0.7123 (tm-30) REVERT: F 133 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7175 (mm-30) outliers start: 31 outliers final: 12 residues processed: 139 average time/residue: 0.6136 time to fit residues: 89.8613 Evaluate side-chains 147 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.197083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123277 restraints weight = 9633.588| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.84 r_work: 0.2853 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8877 Z= 0.105 Angle : 0.486 5.826 12012 Z= 0.261 Chirality : 0.045 0.141 1308 Planarity : 0.004 0.030 1572 Dihedral : 4.545 23.795 1224 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.80 % Allowed : 11.57 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1143 helix: -5.09 (0.23), residues: 18 sheet: -0.34 (0.21), residues: 498 loop : -0.22 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.010 0.001 TYR B 108 PHE 0.008 0.001 PHE C 96 TRP 0.010 0.001 TRP A 48 HIS 0.001 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 8871) covalent geometry : angle 0.48562 / 0.26 (12000) SS BOND : bond 0.00391 / 0.19 ( 6) SS BOND : angle 0.70887 / 0.40 ( 12) hydrogen bonds : bond 0.02765 / 1.75 ( 333) hydrogen bonds : angle 5.16153 / 3.55 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7678 (t0) cc_final: 0.7213 (m-30) REVERT: A 24 LYS cc_start: 0.8138 (tttt) cc_final: 0.7627 (ttmt) REVERT: A 44 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6501 (ttpt) REVERT: A 47 LYS cc_start: 0.8311 (tttt) cc_final: 0.7858 (mttp) REVERT: A 58 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: A 74 GLU cc_start: 0.7564 (tt0) cc_final: 0.6937 (tp30) REVERT: A 130 THR cc_start: 0.8447 (m) cc_final: 0.8107 (p) REVERT: A 134 LYS cc_start: 0.7894 (mttt) cc_final: 0.7374 (tptp) REVERT: A 149 LYS cc_start: 0.7979 (tttt) cc_final: 0.7746 (mtpt) REVERT: A 179 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (ttp80) REVERT: B 1 MET cc_start: 0.5435 (mtm) cc_final: 0.5185 (mtp) REVERT: B 24 LYS cc_start: 0.8114 (tttt) cc_final: 0.7650 (tttt) REVERT: B 44 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6455 (ttpt) REVERT: B 47 LYS cc_start: 0.8245 (tttt) cc_final: 0.7764 (mttp) REVERT: B 58 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: B 74 GLU cc_start: 0.7556 (tt0) cc_final: 0.6910 (tp30) REVERT: B 130 THR cc_start: 0.8508 (m) cc_final: 0.8189 (p) REVERT: B 179 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8143 (ttp80) REVERT: B 228 LYS cc_start: 0.7463 (tttt) cc_final: 0.7058 (tttp) REVERT: C 24 LYS cc_start: 0.8210 (tttt) cc_final: 0.7487 (ttpt) REVERT: C 44 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6357 (ttpt) REVERT: C 47 LYS cc_start: 0.8204 (tttt) cc_final: 0.7764 (mmtp) REVERT: C 58 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: C 74 GLU cc_start: 0.7476 (tt0) cc_final: 0.6917 (tp30) REVERT: C 134 LYS cc_start: 0.7878 (mttt) cc_final: 0.7481 (tptp) REVERT: C 179 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8147 (ttp80) REVERT: C 228 LYS cc_start: 0.7620 (tttt) cc_final: 0.7160 (tttt) REVERT: D 1 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7561 (ttm) REVERT: D 2 GLU cc_start: 0.8399 (tt0) cc_final: 0.7635 (tt0) REVERT: D 4 LYS cc_start: 0.8200 (mttt) cc_final: 0.7824 (mtpp) REVERT: D 26 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7568 (t) REVERT: D 40 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5747 (pm20) REVERT: D 42 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5918 (tp30) REVERT: D 51 GLU cc_start: 0.6492 (tt0) cc_final: 0.5868 (tp30) REVERT: E 2 GLU cc_start: 0.8414 (tt0) cc_final: 0.7660 (tm-30) REVERT: E 4 LYS cc_start: 0.8267 (mttt) cc_final: 0.7639 (mttp) REVERT: E 26 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7485 (t) REVERT: F 2 GLU cc_start: 0.8472 (tt0) cc_final: 0.7620 (tm-30) REVERT: F 4 LYS cc_start: 0.8201 (mttt) cc_final: 0.7648 (mttp) REVERT: F 51 GLU cc_start: 0.6356 (tt0) cc_final: 0.5816 (tp30) REVERT: F 132 GLU cc_start: 0.7642 (mp0) cc_final: 0.7108 (tm-30) REVERT: F 133 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7134 (mm-30) outliers start: 17 outliers final: 6 residues processed: 139 average time/residue: 0.6491 time to fit residues: 95.2958 Evaluate side-chains 145 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.194153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116743 restraints weight = 9591.590| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.51 r_work: 0.2818 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8877 Z= 0.191 Angle : 0.536 5.787 12012 Z= 0.287 Chirality : 0.046 0.146 1308 Planarity : 0.004 0.033 1572 Dihedral : 4.602 23.216 1224 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.20 % Rotamer: Outliers : 3.29 % Allowed : 10.83 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.25), residues: 1143 helix: -5.10 (0.22), residues: 18 sheet: -0.22 (0.22), residues: 483 loop : -0.15 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 79 TYR 0.014 0.002 TYR C 216 PHE 0.011 0.002 PHE C 223 TRP 0.012 0.002 TRP B 48 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8871) covalent geometry : angle 0.53480 / 0.29 (12000) SS BOND : bond 0.00571 / 0.30 ( 6) SS BOND : angle 1.38685 / 0.80 ( 12) hydrogen bonds : bond 0.03219 / 2.08 ( 333) hydrogen bonds : angle 5.38530 / 3.71 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8155 (tttt) cc_final: 0.7632 (ttmt) REVERT: A 44 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6632 (ttpt) REVERT: A 47 LYS cc_start: 0.8325 (tttt) cc_final: 0.7831 (mttp) REVERT: A 58 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 74 GLU cc_start: 0.7563 (tt0) cc_final: 0.6997 (tp30) REVERT: A 130 THR cc_start: 0.8445 (m) cc_final: 0.8120 (p) REVERT: A 134 LYS cc_start: 0.7958 (mttt) cc_final: 0.7402 (tptp) REVERT: A 149 LYS cc_start: 0.8021 (tttt) cc_final: 0.7771 (mtpt) REVERT: A 179 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7215 (mtp85) REVERT: B 1 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.5284 (mtp) REVERT: B 44 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6528 (ttpt) REVERT: B 47 LYS cc_start: 0.8242 (tttt) cc_final: 0.7758 (mttp) REVERT: B 58 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: B 74 GLU cc_start: 0.7562 (tt0) cc_final: 0.6943 (tp30) REVERT: B 130 THR cc_start: 0.8492 (m) cc_final: 0.8193 (p) REVERT: B 133 GLN cc_start: 0.7790 (mt0) cc_final: 0.7560 (pm20) REVERT: B 167 GLN cc_start: 0.8063 (mt0) cc_final: 0.7715 (mt0) REVERT: B 179 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7380 (mtp85) REVERT: B 228 LYS cc_start: 0.7593 (tttt) cc_final: 0.7207 (tttp) REVERT: C 24 LYS cc_start: 0.8224 (tttt) cc_final: 0.7850 (ttmt) REVERT: C 44 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6486 (ttpt) REVERT: C 47 LYS cc_start: 0.8184 (tttt) cc_final: 0.7726 (mttp) REVERT: C 58 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: C 74 GLU cc_start: 0.7440 (tt0) cc_final: 0.6855 (tp30) REVERT: C 134 LYS cc_start: 0.7901 (mttt) cc_final: 0.7481 (tptp) REVERT: C 179 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7756 (mtp85) REVERT: C 228 LYS cc_start: 0.7731 (tttt) cc_final: 0.7200 (tttt) REVERT: D 2 GLU cc_start: 0.8369 (tt0) cc_final: 0.7649 (tt0) REVERT: D 4 LYS cc_start: 0.8226 (mttt) cc_final: 0.7832 (mtpp) REVERT: D 40 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5759 (pm20) REVERT: D 42 GLU cc_start: 0.6242 (mt-10) cc_final: 0.5891 (tp30) REVERT: D 50 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 51 GLU cc_start: 0.6641 (tt0) cc_final: 0.5860 (tp30) REVERT: E 2 GLU cc_start: 0.8422 (tt0) cc_final: 0.7659 (tm-30) REVERT: E 4 LYS cc_start: 0.8309 (mttt) cc_final: 0.7657 (mtpp) REVERT: E 16 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: F 2 GLU cc_start: 0.8457 (tt0) cc_final: 0.7637 (tm-30) REVERT: F 4 LYS cc_start: 0.8212 (mttt) cc_final: 0.7690 (mttp) REVERT: F 50 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7200 (mm-30) REVERT: F 51 GLU cc_start: 0.6378 (tt0) cc_final: 0.5797 (tp30) REVERT: F 132 GLU cc_start: 0.7642 (mp0) cc_final: 0.7113 (tm-30) REVERT: F 133 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7145 (mm-30) outliers start: 31 outliers final: 12 residues processed: 145 average time/residue: 0.6020 time to fit residues: 92.0946 Evaluate side-chains 152 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN E 49 GLN F 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.196000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122515 restraints weight = 9490.611| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.57 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8877 Z= 0.119 Angle : 0.488 5.769 12012 Z= 0.262 Chirality : 0.045 0.140 1308 Planarity : 0.003 0.031 1572 Dihedral : 4.384 22.520 1224 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.36 % Favored : 97.46 % Rotamer: Outliers : 3.08 % Allowed : 11.46 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1143 helix: -5.10 (0.21), residues: 18 sheet: -0.30 (0.22), residues: 489 loop : 0.03 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.013 0.001 TYR B 55 PHE 0.010 0.001 PHE F 45 TRP 0.010 0.001 TRP B 48 HIS 0.001 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8871) covalent geometry : angle 0.48680 / 0.26 (12000) SS BOND : bond 0.00329 / 0.17 ( 6) SS BOND : angle 1.10132 / 0.64 ( 12) hydrogen bonds : bond 0.02795 / 1.78 ( 333) hydrogen bonds : angle 5.12577 / 3.53 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8147 (tttt) cc_final: 0.7629 (ttmt) REVERT: A 44 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6558 (ttpt) REVERT: A 47 LYS cc_start: 0.8311 (tttt) cc_final: 0.7830 (mttp) REVERT: A 58 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: A 74 GLU cc_start: 0.7586 (tt0) cc_final: 0.6978 (tp30) REVERT: A 130 THR cc_start: 0.8461 (m) cc_final: 0.8155 (p) REVERT: A 134 LYS cc_start: 0.7897 (mttt) cc_final: 0.7415 (tptp) REVERT: A 149 LYS cc_start: 0.7985 (tttt) cc_final: 0.7769 (mtpt) REVERT: A 179 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: B 44 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6576 (ttpt) REVERT: B 47 LYS cc_start: 0.8223 (tttt) cc_final: 0.7751 (mttp) REVERT: B 58 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 74 GLU cc_start: 0.7540 (tt0) cc_final: 0.6921 (tp30) REVERT: B 130 THR cc_start: 0.8480 (m) cc_final: 0.8248 (p) REVERT: B 179 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8151 (ttp80) REVERT: B 228 LYS cc_start: 0.7536 (tttt) cc_final: 0.7119 (tttp) REVERT: C 24 LYS cc_start: 0.8197 (tttt) cc_final: 0.7827 (ttmt) REVERT: C 44 LYS cc_start: 0.7094 (mmtt) cc_final: 0.6456 (ttpt) REVERT: C 47 LYS cc_start: 0.8221 (tttt) cc_final: 0.7770 (mmtp) REVERT: C 58 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: C 74 GLU cc_start: 0.7440 (tt0) cc_final: 0.6846 (tp30) REVERT: C 134 LYS cc_start: 0.7832 (mttt) cc_final: 0.7429 (tptp) REVERT: C 179 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8161 (ttp80) REVERT: C 228 LYS cc_start: 0.7665 (tttt) cc_final: 0.7199 (tttt) REVERT: D 2 GLU cc_start: 0.8395 (tt0) cc_final: 0.7674 (tt0) REVERT: D 4 LYS cc_start: 0.8157 (mttt) cc_final: 0.7810 (mtpp) REVERT: D 26 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7523 (t) REVERT: D 40 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5778 (pm20) REVERT: D 50 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7242 (mm-30) REVERT: D 51 GLU cc_start: 0.6677 (tt0) cc_final: 0.5833 (tp30) REVERT: E 2 GLU cc_start: 0.8404 (tt0) cc_final: 0.7648 (tm-30) REVERT: E 4 LYS cc_start: 0.8255 (mttt) cc_final: 0.7651 (mtpp) REVERT: E 16 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: F 2 GLU cc_start: 0.8488 (tt0) cc_final: 0.7681 (tm-30) REVERT: F 4 LYS cc_start: 0.8221 (mttt) cc_final: 0.7698 (mttp) REVERT: F 50 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7277 (mm-30) REVERT: F 51 GLU cc_start: 0.6359 (tt0) cc_final: 0.5757 (tp30) REVERT: F 132 GLU cc_start: 0.7590 (mp0) cc_final: 0.7091 (tm-30) REVERT: F 133 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7118 (mm-30) outliers start: 29 outliers final: 11 residues processed: 142 average time/residue: 0.6524 time to fit residues: 97.5477 Evaluate side-chains 151 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 49 GLN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.194484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117357 restraints weight = 9631.946| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.53 r_work: 0.2843 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8877 Z= 0.161 Angle : 0.510 5.698 12012 Z= 0.273 Chirality : 0.046 0.140 1308 Planarity : 0.004 0.031 1572 Dihedral : 4.414 21.457 1224 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.20 % Rotamer: Outliers : 2.97 % Allowed : 11.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1143 helix: -5.10 (0.21), residues: 18 sheet: -0.17 (0.22), residues: 474 loop : -0.04 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.013 0.002 TYR B 216 PHE 0.013 0.001 PHE D 45 TRP 0.011 0.002 TRP B 48 HIS 0.001 0.000 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8871) covalent geometry : angle 0.50885 / 0.27 (12000) SS BOND : bond 0.00483 / 0.25 ( 6) SS BOND : angle 1.23496 / 0.71 ( 12) hydrogen bonds : bond 0.03012 / 1.94 ( 333) hydrogen bonds : angle 5.24120 / 3.61 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8139 (tttt) cc_final: 0.7613 (ttmt) REVERT: A 44 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6641 (ttpt) REVERT: A 47 LYS cc_start: 0.8306 (tttt) cc_final: 0.7799 (mttp) REVERT: A 58 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 74 GLU cc_start: 0.7548 (tt0) cc_final: 0.6940 (tp30) REVERT: A 130 THR cc_start: 0.8451 (m) cc_final: 0.8138 (p) REVERT: A 134 LYS cc_start: 0.7895 (mttt) cc_final: 0.7387 (tptp) REVERT: A 149 LYS cc_start: 0.7961 (tttt) cc_final: 0.7725 (mtpt) REVERT: B 44 LYS cc_start: 0.7073 (mmtt) cc_final: 0.6566 (ttpt) REVERT: B 47 LYS cc_start: 0.8201 (tttt) cc_final: 0.7725 (mttp) REVERT: B 58 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: B 61 TYR cc_start: 0.9130 (m-80) cc_final: 0.8905 (m-80) REVERT: B 74 GLU cc_start: 0.7568 (tt0) cc_final: 0.6968 (tp30) REVERT: B 130 THR cc_start: 0.8439 (m) cc_final: 0.8203 (p) REVERT: B 228 LYS cc_start: 0.7517 (tttt) cc_final: 0.7142 (tttp) REVERT: C 24 LYS cc_start: 0.8194 (tttt) cc_final: 0.7819 (ttmt) REVERT: C 44 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6481 (ttpt) REVERT: C 47 LYS cc_start: 0.8199 (tttt) cc_final: 0.7744 (mttp) REVERT: C 58 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: C 74 GLU cc_start: 0.7390 (tt0) cc_final: 0.6768 (tp30) REVERT: C 134 LYS cc_start: 0.7834 (mttt) cc_final: 0.7431 (tptp) REVERT: C 228 LYS cc_start: 0.7674 (tttt) cc_final: 0.7173 (tttt) REVERT: D 2 GLU cc_start: 0.8387 (tt0) cc_final: 0.7653 (tt0) REVERT: D 4 LYS cc_start: 0.8224 (mttt) cc_final: 0.7834 (mtpp) REVERT: D 40 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5769 (pm20) REVERT: D 50 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7279 (mm-30) REVERT: D 51 GLU cc_start: 0.6655 (tt0) cc_final: 0.5886 (tp30) REVERT: D 133 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: E 2 GLU cc_start: 0.8434 (tt0) cc_final: 0.7662 (tm-30) REVERT: E 4 LYS cc_start: 0.8271 (mttt) cc_final: 0.7606 (mtpp) REVERT: E 16 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: E 50 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 51 GLU cc_start: 0.6905 (tt0) cc_final: 0.6358 (tp30) REVERT: F 2 GLU cc_start: 0.8464 (tt0) cc_final: 0.7647 (tm-30) REVERT: F 4 LYS cc_start: 0.8221 (mttt) cc_final: 0.7702 (mttp) REVERT: F 50 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7227 (mm-30) REVERT: F 51 GLU cc_start: 0.6407 (tt0) cc_final: 0.5886 (tp30) REVERT: F 132 GLU cc_start: 0.7602 (mp0) cc_final: 0.7104 (tm-30) REVERT: F 133 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7122 (mm-30) outliers start: 28 outliers final: 13 residues processed: 146 average time/residue: 0.6400 time to fit residues: 98.6065 Evaluate side-chains 151 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN E 49 GLN F 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.193281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120824 restraints weight = 9509.028| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.77 r_work: 0.2790 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8877 Z= 0.210 Angle : 0.551 5.186 12012 Z= 0.294 Chirality : 0.049 0.355 1308 Planarity : 0.004 0.034 1572 Dihedral : 4.549 21.703 1224 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.15 % Favored : 96.68 % Rotamer: Outliers : 2.97 % Allowed : 12.53 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1143 helix: -5.09 (0.21), residues: 18 sheet: -0.19 (0.22), residues: 477 loop : -0.09 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 143 TYR 0.014 0.002 TYR C 216 PHE 0.014 0.002 PHE E 45 TRP 0.012 0.002 TRP B 48 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 8871) covalent geometry : angle 0.54901 / 0.29 (12000) SS BOND : bond 0.00614 / 0.33 ( 6) SS BOND : angle 1.39992 / 0.81 ( 12) hydrogen bonds : bond 0.03250 / 2.11 ( 333) hydrogen bonds : angle 5.38676 / 3.72 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8142 (tttt) cc_final: 0.7622 (ttmt) REVERT: A 44 LYS cc_start: 0.7243 (mmtt) cc_final: 0.6633 (ttpt) REVERT: A 47 LYS cc_start: 0.8337 (tttt) cc_final: 0.7797 (mttp) REVERT: A 58 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 74 GLU cc_start: 0.7533 (tt0) cc_final: 0.6935 (tp30) REVERT: A 130 THR cc_start: 0.8436 (m) cc_final: 0.8111 (p) REVERT: A 134 LYS cc_start: 0.7906 (mttt) cc_final: 0.7387 (tptp) REVERT: A 149 LYS cc_start: 0.8032 (tttt) cc_final: 0.7735 (mtpt) REVERT: B 44 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6608 (ttpt) REVERT: B 47 LYS cc_start: 0.8302 (tttt) cc_final: 0.7800 (mttp) REVERT: B 58 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 74 GLU cc_start: 0.7606 (tt0) cc_final: 0.6966 (tp30) REVERT: B 130 THR cc_start: 0.8430 (m) cc_final: 0.8190 (p) REVERT: B 228 LYS cc_start: 0.7558 (tttt) cc_final: 0.7202 (tttp) REVERT: C 24 LYS cc_start: 0.8213 (tttt) cc_final: 0.7823 (ttmt) REVERT: C 44 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6468 (ttpt) REVERT: C 47 LYS cc_start: 0.8232 (tttt) cc_final: 0.7749 (mttp) REVERT: C 58 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: C 74 GLU cc_start: 0.7393 (tt0) cc_final: 0.6733 (tp30) REVERT: C 134 LYS cc_start: 0.7845 (mttt) cc_final: 0.7418 (tptp) REVERT: C 179 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7770 (mtp85) REVERT: C 228 LYS cc_start: 0.7734 (tttt) cc_final: 0.7256 (tttt) REVERT: D 2 GLU cc_start: 0.8411 (tt0) cc_final: 0.7665 (tt0) REVERT: D 4 LYS cc_start: 0.8252 (mttt) cc_final: 0.7845 (mtpp) REVERT: D 40 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: D 50 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7215 (mm-30) REVERT: D 51 GLU cc_start: 0.6647 (tt0) cc_final: 0.5751 (tp30) REVERT: D 133 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6515 (mm-30) REVERT: E 2 GLU cc_start: 0.8445 (tt0) cc_final: 0.7662 (tm-30) REVERT: E 4 LYS cc_start: 0.8283 (mttt) cc_final: 0.7701 (mtpp) REVERT: E 16 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6873 (pp20) REVERT: E 51 GLU cc_start: 0.6906 (tt0) cc_final: 0.6303 (tp30) REVERT: F 2 GLU cc_start: 0.8502 (tt0) cc_final: 0.7671 (tm-30) REVERT: F 4 LYS cc_start: 0.8237 (mttt) cc_final: 0.7704 (mttp) REVERT: F 50 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7189 (mm-30) REVERT: F 51 GLU cc_start: 0.6485 (tt0) cc_final: 0.5924 (tp30) REVERT: F 132 GLU cc_start: 0.7626 (mp0) cc_final: 0.7089 (tm-30) REVERT: F 133 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7100 (mm-30) outliers start: 28 outliers final: 15 residues processed: 140 average time/residue: 0.6686 time to fit residues: 98.5590 Evaluate side-chains 153 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 49 GLN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116622 restraints weight = 9555.713| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.77 r_work: 0.2803 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8877 Z= 0.220 Angle : 0.559 5.787 12012 Z= 0.299 Chirality : 0.049 0.345 1308 Planarity : 0.004 0.036 1572 Dihedral : 4.586 21.581 1224 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.97 % Allowed : 12.85 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1143 helix: -5.08 (0.21), residues: 18 sheet: -0.20 (0.22), residues: 477 loop : -0.15 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 179 TYR 0.015 0.002 TYR B 216 PHE 0.016 0.002 PHE E 45 TRP 0.012 0.002 TRP B 48 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 ( 8871) covalent geometry : angle 0.55803 / 0.30 (12000) SS BOND : bond 0.00660 / 0.35 ( 6) SS BOND : angle 1.38029 / 0.80 ( 12) hydrogen bonds : bond 0.03301 / 2.15 ( 333) hydrogen bonds : angle 5.45340 / 3.76 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8163 (tttt) cc_final: 0.7649 (ttmt) REVERT: A 44 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6649 (ttpt) REVERT: A 47 LYS cc_start: 0.8348 (tttt) cc_final: 0.7804 (mttp) REVERT: A 58 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 74 GLU cc_start: 0.7604 (tt0) cc_final: 0.6959 (tp30) REVERT: A 130 THR cc_start: 0.8410 (m) cc_final: 0.8076 (p) REVERT: A 134 LYS cc_start: 0.7935 (mttt) cc_final: 0.7364 (tptp) REVERT: A 149 LYS cc_start: 0.8053 (tttt) cc_final: 0.7754 (mtpt) REVERT: B 44 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6619 (ttpt) REVERT: B 47 LYS cc_start: 0.8314 (tttt) cc_final: 0.7816 (mttp) REVERT: B 58 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: B 74 GLU cc_start: 0.7648 (tt0) cc_final: 0.7016 (tp30) REVERT: B 130 THR cc_start: 0.8458 (m) cc_final: 0.8205 (p) REVERT: B 228 LYS cc_start: 0.7562 (tttt) cc_final: 0.7189 (tttp) REVERT: C 24 LYS cc_start: 0.8214 (tttt) cc_final: 0.7458 (ttpt) REVERT: C 44 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6436 (ttpt) REVERT: C 47 LYS cc_start: 0.8231 (tttt) cc_final: 0.7751 (mttp) REVERT: C 58 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: C 74 GLU cc_start: 0.7456 (tt0) cc_final: 0.6790 (tp30) REVERT: C 134 LYS cc_start: 0.7820 (mttt) cc_final: 0.7412 (tptp) REVERT: C 228 LYS cc_start: 0.7735 (tttt) cc_final: 0.7343 (tttt) REVERT: D 2 GLU cc_start: 0.8418 (tt0) cc_final: 0.7683 (tt0) REVERT: D 4 LYS cc_start: 0.8247 (mttt) cc_final: 0.7869 (mtpp) REVERT: D 40 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5819 (pm20) REVERT: D 50 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7222 (mm-30) REVERT: D 51 GLU cc_start: 0.6635 (tt0) cc_final: 0.5728 (tp30) REVERT: D 133 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: E 2 GLU cc_start: 0.8450 (tt0) cc_final: 0.7684 (tm-30) REVERT: E 4 LYS cc_start: 0.8334 (mttt) cc_final: 0.7765 (mtpp) REVERT: E 51 GLU cc_start: 0.6934 (tt0) cc_final: 0.6369 (tp30) REVERT: F 2 GLU cc_start: 0.8495 (tt0) cc_final: 0.7647 (tm-30) REVERT: F 4 LYS cc_start: 0.8230 (mttt) cc_final: 0.7719 (mttp) REVERT: F 50 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7192 (mm-30) REVERT: F 51 GLU cc_start: 0.6479 (tt0) cc_final: 0.5965 (tp30) REVERT: F 132 GLU cc_start: 0.7624 (mp0) cc_final: 0.7080 (tm-30) REVERT: F 133 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7119 (mm-30) outliers start: 28 outliers final: 16 residues processed: 141 average time/residue: 0.5893 time to fit residues: 87.6610 Evaluate side-chains 152 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 49 GLN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.193096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116559 restraints weight = 9612.193| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.52 r_work: 0.2833 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8877 Z= 0.198 Angle : 0.543 5.886 12012 Z= 0.290 Chirality : 0.048 0.315 1308 Planarity : 0.004 0.035 1572 Dihedral : 4.519 21.022 1224 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 13.69 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1143 helix: -4.97 (0.19), residues: 21 sheet: -0.19 (0.22), residues: 477 loop : -0.14 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 179 TYR 0.017 0.002 TYR A 55 PHE 0.012 0.002 PHE E 45 TRP 0.012 0.002 TRP B 48 HIS 0.003 0.001 HIS F 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 8871) covalent geometry : angle 0.54190 / 0.29 (12000) SS BOND : bond 0.00582 / 0.31 ( 6) SS BOND : angle 1.31173 / 0.76 ( 12) hydrogen bonds : bond 0.03184 / 2.06 ( 333) hydrogen bonds : angle 5.39608 / 3.72 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8146 (tttt) cc_final: 0.7627 (ttmt) REVERT: A 44 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6681 (ttpt) REVERT: A 47 LYS cc_start: 0.8294 (tttt) cc_final: 0.7764 (mttp) REVERT: A 58 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 74 GLU cc_start: 0.7579 (tt0) cc_final: 0.6966 (tp30) REVERT: A 130 THR cc_start: 0.8433 (m) cc_final: 0.8107 (p) REVERT: A 134 LYS cc_start: 0.7929 (mttt) cc_final: 0.7374 (tptp) REVERT: A 149 LYS cc_start: 0.8029 (tttt) cc_final: 0.7739 (mtpt) REVERT: B 44 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6691 (ttpt) REVERT: B 47 LYS cc_start: 0.8258 (tttt) cc_final: 0.7749 (mttp) REVERT: B 58 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 74 GLU cc_start: 0.7620 (tt0) cc_final: 0.7004 (tp30) REVERT: B 130 THR cc_start: 0.8427 (m) cc_final: 0.8217 (p) REVERT: B 167 GLN cc_start: 0.8045 (mt0) cc_final: 0.7682 (mt0) REVERT: B 228 LYS cc_start: 0.7557 (tttt) cc_final: 0.7178 (tttp) REVERT: C 24 LYS cc_start: 0.8199 (tttt) cc_final: 0.7441 (ttpt) REVERT: C 44 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6455 (ttpt) REVERT: C 47 LYS cc_start: 0.8191 (tttt) cc_final: 0.7711 (mttp) REVERT: C 58 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 74 GLU cc_start: 0.7437 (tt0) cc_final: 0.6771 (tp30) REVERT: C 134 LYS cc_start: 0.7822 (mttt) cc_final: 0.7396 (tptp) REVERT: C 228 LYS cc_start: 0.7727 (tttt) cc_final: 0.7323 (tttt) REVERT: D 2 GLU cc_start: 0.8413 (tt0) cc_final: 0.7674 (tt0) REVERT: D 4 LYS cc_start: 0.8217 (mttt) cc_final: 0.7837 (mtpp) REVERT: D 40 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5849 (pm20) REVERT: D 50 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 2 GLU cc_start: 0.8440 (tt0) cc_final: 0.7654 (tm-30) REVERT: E 4 LYS cc_start: 0.8302 (mttt) cc_final: 0.7758 (mtpp) REVERT: E 50 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7058 (mm-30) REVERT: E 51 GLU cc_start: 0.6914 (tt0) cc_final: 0.6339 (tp30) REVERT: F 2 GLU cc_start: 0.8461 (tt0) cc_final: 0.7632 (tm-30) REVERT: F 4 LYS cc_start: 0.8199 (mttt) cc_final: 0.7708 (mttp) REVERT: F 50 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7213 (mm-30) REVERT: F 51 GLU cc_start: 0.6503 (tt0) cc_final: 0.5936 (tp30) REVERT: F 132 GLU cc_start: 0.7608 (mp0) cc_final: 0.7076 (tm-30) REVERT: F 133 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7083 (mm-30) outliers start: 21 outliers final: 15 residues processed: 143 average time/residue: 0.6895 time to fit residues: 103.7782 Evaluate side-chains 150 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN E 49 GLN F 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.192116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120182 restraints weight = 9616.921| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.64 r_work: 0.2778 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8877 Z= 0.241 Angle : 0.576 7.037 12012 Z= 0.307 Chirality : 0.049 0.320 1308 Planarity : 0.004 0.037 1572 Dihedral : 4.634 21.469 1224 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 2.65 % Allowed : 13.06 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1143 helix: -4.97 (0.19), residues: 21 sheet: -0.21 (0.23), residues: 477 loop : -0.18 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 179 TYR 0.018 0.002 TYR B 55 PHE 0.012 0.002 PHE F 45 TRP 0.012 0.002 TRP B 48 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 ( 8871) covalent geometry : angle 0.57432 / 0.31 (12000) SS BOND : bond 0.00700 / 0.38 ( 6) SS BOND : angle 1.45903 / 0.84 ( 12) hydrogen bonds : bond 0.03401 / 2.21 ( 333) hydrogen bonds : angle 5.55356 / 3.82 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.72 seconds wall clock time: 69 minutes 58.91 seconds (4198.91 seconds total)