Starting phenix.real_space_refine on Fri Sep 11 02:06:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4y_65646/09_2026/9w4y_65646.cif" } resolution = 2.0 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= 0.008 sd= 0.051 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 41 5.16 5 C 4150 2.51 5 N 1103 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.60, per 1000 atoms: 0.24 Number of scatterers: 6553 At special positions: 0 Unit cell: (92.169, 109.858, 84.721, 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 41 16.00 O 1259 8.00 N 1103 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA2-6 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 287.7 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.9% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 removed outlier: 3.565A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.658A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.642A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.574A pdb=" N ALA B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.099A pdb=" N MET C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.726A pdb=" N ARG C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 50 through 55 Processing helix chain 'E' and resid 201 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 5.640A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.955A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.943A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.943A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.601A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.876A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.257A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 525 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: 0.76 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2113 1.34 - 1.46: 1312 1.46 - 1.57: 3222 1.57 - 1.69: 1 1.69 - 1.81: 68 Bond restraints: 6716 Sorted by residual: bond pdb=" CA ASN C 237 " pdb=" C ASN C 237 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.31e-02 5.83e+03 4.03e+00 bond pdb=" CA GLN C 235 " pdb=" C GLN C 235 " ideal model delta sigma weight residual 1.522 1.499 0.022 1.21e-02 6.83e+03 3.45e+00 bond pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.27e-02 6.20e+03 3.00e+00 bond pdb=" CA SER C 236 " pdb=" CB SER C 236 " ideal model delta sigma weight residual 1.536 1.514 0.021 1.42e-02 4.96e+03 2.29e+00 bond pdb=" CA VAL A 295 " pdb=" C VAL A 295 " ideal model delta sigma weight residual 1.523 1.504 0.018 1.28e-02 6.10e+03 2.07e+00 ... (remaining 6711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 8918 1.19 - 2.38: 168 2.38 - 3.57: 58 3.57 - 4.75: 6 4.75 - 5.94: 4 Bond angle restraints: 9154 Sorted by residual: angle pdb=" N SER C 236 " pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 113.97 108.03 5.94 1.28e+00 6.10e-01 2.16e+01 angle pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 112.60 118.34 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.24e+00 angle pdb=" C ILE A 294 " pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta sigma weight residual 123.12 120.35 2.77 1.30e+00 5.92e-01 4.55e+00 angle pdb=" CA ARG E 205 " pdb=" CB ARG E 205 " pdb=" CG ARG E 205 " ideal model delta sigma weight residual 114.10 117.96 -3.86 2.00e+00 2.50e-01 3.73e+00 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 3780 21.96 - 43.91: 235 43.91 - 65.87: 53 65.87 - 87.82: 15 87.82 - 109.78: 10 Dihedral angle restraints: 4093 sinusoidal: 1693 harmonic: 2400 Sorted by residual: dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual 54.75 -55.03 109.78 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O4 MAN F 4 " ideal model delta sinusoidal sigma weight residual 176.13 66.90 109.23 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C5 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O3 MAN F 4 " ideal model delta sinusoidal sigma weight residual -174.53 -66.18 -108.35 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 826 0.046 - 0.091: 162 0.091 - 0.136: 65 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1055 Sorted by residual: chirality pdb=" C2 SIA G 2 " pdb=" O6 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.44 -0.06 2.00e-02 2.50e+03 7.75e+00 chirality pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" O3 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.41 2.18 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.13 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1052 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 31 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO C 32 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 32 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 32 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 36 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO C 37 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 37 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 37 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO C 93 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.014 5.00e-02 4.00e+02 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3320 2.99 - 3.46: 6086 3.46 - 3.94: 11206 3.94 - 4.42: 13285 4.42 - 4.90: 20866 Nonbonded interactions: 54763 Sorted by model distance: nonbonded pdb=" N GLU A 19 " pdb=" OE1 GLU A 19 " model vdw 2.508 3.120 nonbonded pdb=" C6 GAL G 1 " pdb=" O6 SIA G 2 " model vdw 2.544 2.752 nonbonded pdb=" O5 BMA F 3 " pdb=" O6 BMA F 3 " model vdw 2.554 2.432 nonbonded pdb=" N SER C 236 " pdb=" N ASN C 237 " model vdw 2.570 2.560 nonbonded pdb=" N ASP A 159 " pdb=" OD1 ASP A 159 " model vdw 2.571 3.120 ... (remaining 54758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 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 : 0.002 0.040 6722 Z= 0.114 Angle : 0.487 5.943 9172 Z= 0.254 Chirality : 0.042 0.227 1055 Planarity : 0.004 0.030 1171 Dihedral : 16.410 109.780 2543 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.26 % Allowed : 15.10 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.19 (0.29), residues: 819 helix: -1.75 (0.62), residues: 67 sheet: 0.75 (0.38), residues: 195 loop : -0.19 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.014 0.001 TYR B 31 PHE 0.007 0.001 PHE A 100 TRP 0.007 0.001 TRP B 207 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 6716) covalent geometry : angle 0.48018 / 0.25 ( 9154) hydrogen bonds : bond 0.17795 / 12.66 ( 177) hydrogen bonds : angle 8.76075 / 5.93 ( 525) glycosidic custom : bond 0.00060 / 0.03 ( 1) glycosidic custom : angle 0.21183 / 0.11 ( 3) link_ALPHA1-3 : bond 0.00468 / 0.25 ( 1) link_ALPHA1-3 : angle 3.46174 / 1.77 ( 3) link_ALPHA1-6 : bond 0.00775 / 0.41 ( 1) link_ALPHA1-6 : angle 1.41954 / 0.79 ( 3) link_BETA1-4 : bond 0.00220 / 0.11 ( 2) link_BETA1-4 : angle 1.91671 / 0.93 ( 6) link_BETA1-6 : bond 0.00296 / 0.16 ( 1) link_BETA1-6 : angle 1.15900 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.241 Fit side-chains REVERT: A 19 GLU cc_start: 0.8109 (pm20) cc_final: 0.7711 (pm20) REVERT: A 51 GLN cc_start: 0.9439 (mt0) cc_final: 0.9188 (mt0) REVERT: A 136 MET cc_start: 0.4758 (ttt) cc_final: 0.3848 (mtp) REVERT: B 67 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8257 (ptp-110) REVERT: B 148 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8432 (mptp) REVERT: C 53 MET cc_start: 0.9446 (mtm) cc_final: 0.9160 (mtm) REVERT: C 145 GLU cc_start: 0.8451 (pm20) cc_final: 0.7988 (pm20) REVERT: C 148 MET cc_start: 0.8108 (ppp) cc_final: 0.7778 (pp-130) REVERT: E 205 ARG cc_start: 0.8839 (ppt170) cc_final: 0.8530 (ppt170) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.6054 time to fit residues: 66.5567 Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN B 55 GLN B 131 GLN B 206 GLN B 240 ASN C 160 GLN C 186 ASN C 235 GLN D 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.069067 restraints weight = 9069.332| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.81 r_work: 0.2728 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6722 Z= 0.262 Angle : 0.597 8.223 9172 Z= 0.308 Chirality : 0.047 0.229 1055 Planarity : 0.005 0.056 1171 Dihedral : 9.455 77.409 1064 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.38 % Allowed : 13.43 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.24 (0.28), residues: 819 helix: -1.65 (0.60), residues: 66 sheet: 0.86 (0.38), residues: 188 loop : -0.31 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 12 TYR 0.020 0.002 TYR B 31 PHE 0.013 0.002 PHE A 100 TRP 0.008 0.001 TRP A 249 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 ( 6716) covalent geometry : angle 0.59199 / 0.31 ( 9154) hydrogen bonds : bond 0.04686 / 3.29 ( 177) hydrogen bonds : angle 6.49756 / 4.50 ( 525) glycosidic custom : bond 0.00086 / 0.05 ( 1) glycosidic custom : angle 0.81598 / 0.43 ( 3) link_ALPHA1-3 : bond 0.00317 / 0.17 ( 1) link_ALPHA1-3 : angle 2.56561 / 1.30 ( 3) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 1) link_ALPHA1-6 : angle 1.46405 / 0.83 ( 3) link_BETA1-4 : bond 0.00350 / 0.18 ( 2) link_BETA1-4 : angle 2.07056 / 1.01 ( 6) link_BETA1-6 : bond 0.00103 / 0.05 ( 1) link_BETA1-6 : angle 1.18219 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.216 Fit side-chains REVERT: A 2 GLU cc_start: 0.8495 (tt0) cc_final: 0.8234 (tt0) REVERT: A 51 GLN cc_start: 0.9428 (mt0) cc_final: 0.9192 (mt0) REVERT: A 136 MET cc_start: 0.4919 (ttt) cc_final: 0.3988 (ttp) REVERT: B 72 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8566 (mm-30) REVERT: C 53 MET cc_start: 0.9537 (mtm) cc_final: 0.9245 (mtm) REVERT: C 145 GLU cc_start: 0.8519 (pm20) cc_final: 0.8062 (pm20) REVERT: C 148 MET cc_start: 0.8193 (ppp) cc_final: 0.7883 (pp-130) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.6068 time to fit residues: 66.0400 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 HIS C 101 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.072012 restraints weight = 9032.538| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.82 r_work: 0.2781 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6722 Z= 0.108 Angle : 0.492 4.734 9172 Z= 0.253 Chirality : 0.042 0.190 1055 Planarity : 0.004 0.028 1171 Dihedral : 6.742 77.029 1055 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 13.29 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.11 (0.28), residues: 819 helix: -1.35 (0.65), residues: 60 sheet: 0.92 (0.37), residues: 187 loop : -0.24 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 205 TYR 0.016 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6716) covalent geometry : angle 0.48532 / 0.25 ( 9154) hydrogen bonds : bond 0.03565 / 2.46 ( 177) hydrogen bonds : angle 5.93137 / 4.14 ( 525) glycosidic custom : bond 0.00028 / 0.01 ( 1) glycosidic custom : angle 0.55533 / 0.29 ( 3) link_ALPHA1-3 : bond 0.00396 / 0.21 ( 1) link_ALPHA1-3 : angle 3.14968 / 1.66 ( 3) link_ALPHA1-6 : bond 0.00584 / 0.31 ( 1) link_ALPHA1-6 : angle 1.42420 / 0.80 ( 3) link_BETA1-4 : bond 0.00125 / 0.06 ( 2) link_BETA1-4 : angle 1.96150 / 0.95 ( 6) link_BETA1-6 : bond 0.00313 / 0.16 ( 1) link_BETA1-6 : angle 1.16701 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.268 Fit side-chains REVERT: A 2 GLU cc_start: 0.8477 (tt0) cc_final: 0.8234 (tt0) REVERT: A 51 GLN cc_start: 0.9423 (mt0) cc_final: 0.9178 (mt0) REVERT: A 136 MET cc_start: 0.4785 (ttt) cc_final: 0.3899 (mtp) REVERT: B 72 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: C 53 MET cc_start: 0.9479 (mtm) cc_final: 0.9147 (mtm) REVERT: C 145 GLU cc_start: 0.8507 (pm20) cc_final: 0.8047 (pm20) REVERT: C 148 MET cc_start: 0.8174 (ppp) cc_final: 0.7807 (pp-130) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 0.5854 time to fit residues: 65.0665 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.0020 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 0.0270 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.5450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071733 restraints weight = 9051.934| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.82 r_work: 0.2777 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6722 Z= 0.125 Angle : 0.501 5.200 9172 Z= 0.258 Chirality : 0.043 0.211 1055 Planarity : 0.004 0.037 1171 Dihedral : 6.484 76.255 1054 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.82 % Allowed : 13.99 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.07 (0.28), residues: 819 helix: -1.38 (0.63), residues: 66 sheet: 0.97 (0.37), residues: 187 loop : -0.20 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.005 0.001 TRP A 249 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6716) covalent geometry : angle 0.49396 / 0.26 ( 9154) hydrogen bonds : bond 0.03464 / 2.39 ( 177) hydrogen bonds : angle 5.77874 / 4.04 ( 525) glycosidic custom : bond 0.00075 / 0.04 ( 1) glycosidic custom : angle 0.69758 / 0.36 ( 3) link_ALPHA1-3 : bond 0.00045 / 0.02 ( 1) link_ALPHA1-3 : angle 3.46022 / 1.79 ( 3) link_ALPHA1-6 : bond 0.00543 / 0.29 ( 1) link_ALPHA1-6 : angle 1.41715 / 0.79 ( 3) link_BETA1-4 : bond 0.00133 / 0.06 ( 2) link_BETA1-4 : angle 1.93850 / 0.91 ( 6) link_BETA1-6 : bond 0.00282 / 0.15 ( 1) link_BETA1-6 : angle 1.18102 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.269 Fit side-chains REVERT: A 2 GLU cc_start: 0.8486 (tt0) cc_final: 0.8245 (tt0) REVERT: A 51 GLN cc_start: 0.9429 (mt0) cc_final: 0.9185 (mt0) REVERT: A 136 MET cc_start: 0.4743 (ttt) cc_final: 0.3860 (mtp) REVERT: B 72 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: C 53 MET cc_start: 0.9476 (mtm) cc_final: 0.9183 (mtm) REVERT: C 145 GLU cc_start: 0.8506 (pm20) cc_final: 0.8034 (pm20) REVERT: C 148 MET cc_start: 0.8190 (ppp) cc_final: 0.7823 (pp-130) outliers start: 13 outliers final: 12 residues processed: 100 average time/residue: 0.6032 time to fit residues: 63.1296 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.0040 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.069646 restraints weight = 9194.224| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.83 r_work: 0.2740 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6722 Z= 0.219 Angle : 0.558 5.475 9172 Z= 0.290 Chirality : 0.046 0.219 1055 Planarity : 0.004 0.045 1171 Dihedral : 6.720 75.976 1054 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.52 % Allowed : 13.29 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.19 (0.28), residues: 819 helix: -1.47 (0.62), residues: 66 sheet: 0.89 (0.37), residues: 188 loop : -0.29 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 12 TYR 0.019 0.002 TYR B 31 PHE 0.012 0.002 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 6716) covalent geometry : angle 0.55154 / 0.29 ( 9154) hydrogen bonds : bond 0.03960 / 2.74 ( 177) hydrogen bonds : angle 5.93573 / 4.14 ( 525) glycosidic custom : bond 0.00064 / 0.03 ( 1) glycosidic custom : angle 0.80111 / 0.42 ( 3) link_ALPHA1-3 : bond 0.00048 / 0.03 ( 1) link_ALPHA1-3 : angle 3.40430 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00506 / 0.27 ( 1) link_ALPHA1-6 : angle 1.41960 / 0.79 ( 3) link_BETA1-4 : bond 0.00270 / 0.14 ( 2) link_BETA1-4 : angle 1.93257 / 0.92 ( 6) link_BETA1-6 : bond 0.00174 / 0.09 ( 1) link_BETA1-6 : angle 1.15821 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.241 Fit side-chains REVERT: A 2 GLU cc_start: 0.8507 (tt0) cc_final: 0.8264 (tt0) REVERT: A 51 GLN cc_start: 0.9432 (mt0) cc_final: 0.9155 (mt0) REVERT: A 136 MET cc_start: 0.4767 (ttt) cc_final: 0.3886 (mtp) REVERT: B 72 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: C 53 MET cc_start: 0.9530 (mtm) cc_final: 0.9255 (mtm) REVERT: C 145 GLU cc_start: 0.8534 (pm20) cc_final: 0.8058 (pm20) REVERT: C 148 MET cc_start: 0.8180 (ppp) cc_final: 0.7879 (pp-130) REVERT: E 205 ARG cc_start: 0.8815 (ppt170) cc_final: 0.8221 (ppt170) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.6399 time to fit residues: 68.9519 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.071467 restraints weight = 9108.409| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.82 r_work: 0.2771 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6722 Z= 0.126 Angle : 0.503 5.623 9172 Z= 0.260 Chirality : 0.043 0.212 1055 Planarity : 0.004 0.028 1171 Dihedral : 6.537 75.166 1054 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.96 % Allowed : 13.71 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.11 (0.28), residues: 819 helix: -1.39 (0.63), residues: 66 sheet: 0.97 (0.37), residues: 187 loop : -0.25 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.016 0.001 TYR B 31 PHE 0.011 0.001 PHE C 215 TRP 0.006 0.001 TRP B 207 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6716) covalent geometry : angle 0.49642 / 0.26 ( 9154) hydrogen bonds : bond 0.03422 / 2.35 ( 177) hydrogen bonds : angle 5.71639 / 4.00 ( 525) glycosidic custom : bond 0.00122 / 0.06 ( 1) glycosidic custom : angle 0.72424 / 0.38 ( 3) link_ALPHA1-3 : bond 0.00068 / 0.04 ( 1) link_ALPHA1-3 : angle 3.43677 / 1.77 ( 3) link_ALPHA1-6 : bond 0.00577 / 0.30 ( 1) link_ALPHA1-6 : angle 1.41394 / 0.79 ( 3) link_BETA1-4 : bond 0.00180 / 0.09 ( 2) link_BETA1-4 : angle 1.71912 / 0.84 ( 6) link_BETA1-6 : bond 0.00285 / 0.15 ( 1) link_BETA1-6 : angle 1.15253 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.206 Fit side-chains REVERT: A 2 GLU cc_start: 0.8468 (tt0) cc_final: 0.8222 (tt0) REVERT: A 51 GLN cc_start: 0.9427 (mt0) cc_final: 0.9184 (mt0) REVERT: A 136 MET cc_start: 0.4687 (ttt) cc_final: 0.3849 (mtp) REVERT: A 260 MET cc_start: 0.9288 (mtp) cc_final: 0.8821 (mtp) REVERT: B 72 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: C 53 MET cc_start: 0.9491 (mtm) cc_final: 0.9216 (mtm) REVERT: C 145 GLU cc_start: 0.8517 (pm20) cc_final: 0.8045 (pm20) REVERT: C 148 MET cc_start: 0.8184 (ppp) cc_final: 0.7830 (pp-130) REVERT: E 205 ARG cc_start: 0.8718 (ppt170) cc_final: 0.8174 (ppt170) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.6082 time to fit residues: 64.3586 Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.072202 restraints weight = 8946.130| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.80 r_work: 0.2785 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6722 Z= 0.112 Angle : 0.494 5.961 9172 Z= 0.253 Chirality : 0.043 0.211 1055 Planarity : 0.004 0.039 1171 Dihedral : 6.382 74.063 1054 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 13.85 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.05 (0.28), residues: 819 helix: -1.27 (0.65), residues: 60 sheet: 0.99 (0.37), residues: 187 loop : -0.22 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 12 TYR 0.016 0.001 TYR B 31 PHE 0.011 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6716) covalent geometry : angle 0.48738 / 0.25 ( 9154) hydrogen bonds : bond 0.03242 / 2.23 ( 177) hydrogen bonds : angle 5.58150 / 3.90 ( 525) glycosidic custom : bond 0.00124 / 0.07 ( 1) glycosidic custom : angle 0.74372 / 0.39 ( 3) link_ALPHA1-3 : bond 0.00150 / 0.08 ( 1) link_ALPHA1-3 : angle 3.39527 / 1.75 ( 3) link_ALPHA1-6 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-6 : angle 1.42867 / 0.79 ( 3) link_BETA1-4 : bond 0.00226 / 0.11 ( 2) link_BETA1-4 : angle 1.70869 / 0.83 ( 6) link_BETA1-6 : bond 0.00292 / 0.15 ( 1) link_BETA1-6 : angle 1.17483 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.272 Fit side-chains REVERT: A 2 GLU cc_start: 0.8455 (tt0) cc_final: 0.8203 (tt0) REVERT: A 51 GLN cc_start: 0.9425 (mt0) cc_final: 0.9181 (mt0) REVERT: A 136 MET cc_start: 0.4628 (ttt) cc_final: 0.3805 (mtp) REVERT: B 72 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: C 53 MET cc_start: 0.9461 (mtm) cc_final: 0.9211 (mtm) REVERT: C 145 GLU cc_start: 0.8506 (pm20) cc_final: 0.8036 (pm20) REVERT: C 148 MET cc_start: 0.8189 (ppp) cc_final: 0.7833 (pp-130) REVERT: E 205 ARG cc_start: 0.8688 (ppt170) cc_final: 0.8254 (ppt170) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.5946 time to fit residues: 62.3218 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.069824 restraints weight = 9091.248| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.82 r_work: 0.2742 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6722 Z= 0.215 Angle : 0.554 5.816 9172 Z= 0.287 Chirality : 0.045 0.223 1055 Planarity : 0.004 0.044 1171 Dihedral : 6.629 73.852 1054 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.10 % Allowed : 13.99 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.19 (0.28), residues: 819 helix: -1.45 (0.61), residues: 66 sheet: 0.88 (0.37), residues: 188 loop : -0.28 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 12 TYR 0.020 0.002 TYR B 31 PHE 0.012 0.002 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 6716) covalent geometry : angle 0.54813 / 0.29 ( 9154) hydrogen bonds : bond 0.03846 / 2.66 ( 177) hydrogen bonds : angle 5.85173 / 4.08 ( 525) glycosidic custom : bond 0.00072 / 0.04 ( 1) glycosidic custom : angle 0.83784 / 0.45 ( 3) link_ALPHA1-3 : bond 0.00028 / 0.01 ( 1) link_ALPHA1-3 : angle 3.40794 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00501 / 0.26 ( 1) link_ALPHA1-6 : angle 1.43173 / 0.79 ( 3) link_BETA1-4 : bond 0.00265 / 0.13 ( 2) link_BETA1-4 : angle 1.84542 / 0.88 ( 6) link_BETA1-6 : bond 0.00177 / 0.09 ( 1) link_BETA1-6 : angle 1.19533 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.265 Fit side-chains REVERT: A 2 GLU cc_start: 0.8486 (tt0) cc_final: 0.8245 (tt0) REVERT: A 51 GLN cc_start: 0.9435 (mt0) cc_final: 0.9162 (mt0) REVERT: A 136 MET cc_start: 0.4674 (ttt) cc_final: 0.3818 (mtp) REVERT: B 72 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8570 (mm-30) REVERT: C 53 MET cc_start: 0.9525 (mtm) cc_final: 0.9238 (mtm) REVERT: C 145 GLU cc_start: 0.8533 (pm20) cc_final: 0.8055 (pm20) REVERT: C 148 MET cc_start: 0.8227 (ppp) cc_final: 0.7883 (pp-130) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.5563 time to fit residues: 58.8284 Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 55 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.073746 restraints weight = 9047.360| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.81 r_work: 0.2812 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6722 Z= 0.087 Angle : 0.480 5.284 9172 Z= 0.245 Chirality : 0.042 0.206 1055 Planarity : 0.004 0.036 1171 Dihedral : 6.260 72.229 1054 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 14.55 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.06 (0.28), residues: 819 helix: -1.32 (0.65), residues: 61 sheet: 0.99 (0.37), residues: 187 loop : -0.21 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.013 0.001 TYR B 31 PHE 0.008 0.001 PHE C 215 TRP 0.008 0.001 TRP B 207 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 6716) covalent geometry : angle 0.47301 / 0.24 ( 9154) hydrogen bonds : bond 0.02965 / 2.02 ( 177) hydrogen bonds : angle 5.42164 / 3.79 ( 525) glycosidic custom : bond 0.00146 / 0.08 ( 1) glycosidic custom : angle 0.67373 / 0.36 ( 3) link_ALPHA1-3 : bond 0.00105 / 0.06 ( 1) link_ALPHA1-3 : angle 3.42865 / 1.77 ( 3) link_ALPHA1-6 : bond 0.00549 / 0.29 ( 1) link_ALPHA1-6 : angle 1.42023 / 0.79 ( 3) link_BETA1-4 : bond 0.00180 / 0.09 ( 2) link_BETA1-4 : angle 1.59674 / 0.80 ( 6) link_BETA1-6 : bond 0.00358 / 0.19 ( 1) link_BETA1-6 : angle 1.12496 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.278 Fit side-chains REVERT: A 2 GLU cc_start: 0.8465 (tt0) cc_final: 0.8202 (tt0) REVERT: A 51 GLN cc_start: 0.9417 (mt0) cc_final: 0.9163 (mt0) REVERT: A 136 MET cc_start: 0.4502 (ttt) cc_final: 0.3696 (mtp) REVERT: A 260 MET cc_start: 0.9235 (mtp) cc_final: 0.8855 (mtp) REVERT: B 67 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8344 (ptp-110) REVERT: B 72 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: C 53 MET cc_start: 0.9404 (mtm) cc_final: 0.9166 (mtm) REVERT: C 145 GLU cc_start: 0.8494 (pm20) cc_final: 0.8086 (pm20) REVERT: D 55 GLU cc_start: 0.8939 (tt0) cc_final: 0.8627 (tp30) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.6463 time to fit residues: 68.9754 Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.087710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.071696 restraints weight = 9041.781| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.82 r_work: 0.2776 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6722 Z= 0.138 Angle : 0.511 7.260 9172 Z= 0.262 Chirality : 0.043 0.213 1055 Planarity : 0.004 0.030 1171 Dihedral : 6.322 71.652 1054 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.06 (0.28), residues: 819 helix: -1.39 (0.63), residues: 67 sheet: 0.99 (0.37), residues: 187 loop : -0.20 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.011 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6716) covalent geometry : angle 0.50505 / 0.26 ( 9154) hydrogen bonds : bond 0.03351 / 2.31 ( 177) hydrogen bonds : angle 5.57789 / 3.90 ( 525) glycosidic custom : bond 0.00047 / 0.02 ( 1) glycosidic custom : angle 0.78935 / 0.42 ( 3) link_ALPHA1-3 : bond 0.00172 / 0.09 ( 1) link_ALPHA1-3 : angle 3.33549 / 1.71 ( 3) link_ALPHA1-6 : bond 0.00548 / 0.29 ( 1) link_ALPHA1-6 : angle 1.43497 / 0.79 ( 3) link_BETA1-4 : bond 0.00233 / 0.11 ( 2) link_BETA1-4 : angle 1.72364 / 0.83 ( 6) link_BETA1-6 : bond 0.00246 / 0.13 ( 1) link_BETA1-6 : angle 1.19965 / 0.62 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.261 Fit side-chains REVERT: A 2 GLU cc_start: 0.8474 (tt0) cc_final: 0.8213 (tt0) REVERT: A 51 GLN cc_start: 0.9427 (mt0) cc_final: 0.9182 (mt0) REVERT: A 136 MET cc_start: 0.4539 (ttt) cc_final: 0.3684 (mtp) REVERT: B 67 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8362 (ptp-110) REVERT: B 72 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: C 53 MET cc_start: 0.9468 (mtm) cc_final: 0.9188 (mtm) REVERT: C 145 GLU cc_start: 0.8507 (pm20) cc_final: 0.8097 (pm20) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.6480 time to fit residues: 65.7023 Evaluate side-chains 99 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN C 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.075565 restraints weight = 9019.913| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.83 r_work: 0.2844 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6722 Z= 0.079 Angle : 0.474 6.319 9172 Z= 0.239 Chirality : 0.042 0.205 1055 Planarity : 0.004 0.035 1171 Dihedral : 6.007 69.543 1054 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.03 (0.28), residues: 819 helix: -1.23 (0.65), residues: 61 sheet: 0.81 (0.37), residues: 197 loop : -0.14 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 12 TYR 0.012 0.001 TYR B 31 PHE 0.009 0.001 PHE C 215 TRP 0.008 0.001 TRP B 207 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 ( 6716) covalent geometry : angle 0.46756 / 0.24 ( 9154) hydrogen bonds : bond 0.02755 / 1.87 ( 177) hydrogen bonds : angle 5.25421 / 3.67 ( 525) glycosidic custom : bond 0.00031 / 0.02 ( 1) glycosidic custom : angle 0.65143 / 0.35 ( 3) link_ALPHA1-3 : bond 0.00369 / 0.19 ( 1) link_ALPHA1-3 : angle 3.34742 / 1.73 ( 3) link_ALPHA1-6 : bond 0.00464 / 0.24 ( 1) link_ALPHA1-6 : angle 1.37726 / 0.76 ( 3) link_BETA1-4 : bond 0.00282 / 0.14 ( 2) link_BETA1-4 : angle 1.59525 / 0.80 ( 6) link_BETA1-6 : bond 0.00376 / 0.20 ( 1) link_BETA1-6 : angle 1.12642 / 0.58 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.32 seconds wall clock time: 57 minutes 52.71 seconds (3472.71 seconds total)