Starting phenix.real_space_refine on Thu Sep 10 21:53:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rbu_24402/09_2026/7rbu_24402.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 13 5.16 5 C 2629 2.51 5 N 665 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4107 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2241 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.05, per 1000 atoms: 0.26 Number of scatterers: 4107 At special positions: 0 Unit cell: (86.8, 66.64, 81.2, 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 13 16.00 O 800 8.00 N 665 7.00 C 2629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN B 122 " " NAG B 401 " - " ASN B 234 " " NAG B 402 " - " ASN B 61 " " NAG B 403 " - " ASN B 149 " " NAG C 1 " - " ASN B 17 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 150.2 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.575A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.555A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.829A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 37 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER H 52 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 93 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 121 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.784A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.013A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.330A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 303 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: 0.47 Time building geometry restraints manager: 0.46 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: 1264 1.34 - 1.47: 1167 1.47 - 1.59: 1771 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 4218 Sorted by residual: bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.30e-02 5.92e+03 8.81e+00 bond pdb=" N PHE B 168 " pdb=" CA PHE B 168 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.20e-02 6.94e+03 6.98e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.16e-02 7.43e+03 4.84e+00 ... (remaining 4213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 5204 1.24 - 2.48: 403 2.48 - 3.71: 102 3.71 - 4.95: 25 4.95 - 6.19: 7 Bond angle restraints: 5741 Sorted by residual: angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" O ASN B 165 " ideal model delta sigma weight residual 121.84 116.48 5.36 1.16e+00 7.43e-01 2.14e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" C SER L 56 " pdb=" CA SER L 56 " pdb=" CB SER L 56 " ideal model delta sigma weight residual 116.34 110.15 6.19 1.40e+00 5.10e-01 1.95e+01 angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" N CYS B 166 " ideal model delta sigma weight residual 115.51 119.95 -4.44 1.30e+00 5.92e-01 1.17e+01 angle pdb=" CA ASN B 164 " pdb=" C ASN B 164 " pdb=" O ASN B 164 " ideal model delta sigma weight residual 121.38 117.77 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 5736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2186 17.16 - 34.32: 170 34.32 - 51.48: 41 51.48 - 68.64: 4 68.64 - 85.80: 2 Dihedral angle restraints: 2403 sinusoidal: 925 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 151.53 -58.53 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA CYS B 136 " pdb=" C CYS B 136 " pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 2400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 462 0.046 - 0.092: 136 0.092 - 0.138: 42 0.138 - 0.184: 5 0.184 - 0.230: 2 Chirality restraints: 647 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU B 169 " pdb=" N GLU B 169 " pdb=" C GLU B 169 " pdb=" CB GLU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA SER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB SER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 644 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.81e+00 pdb=" N PRO B 209 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO L 59 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 161 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C SER B 161 " -0.026 2.00e-02 2.50e+03 pdb=" O SER B 161 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 162 " 0.009 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 204 2.71 - 3.26: 3673 3.26 - 3.81: 5933 3.81 - 4.35: 6871 4.35 - 4.90: 12578 Nonbonded interactions: 29259 Sorted by model distance: nonbonded pdb=" OG SER L 52 " pdb=" O GLY L 64 " model vdw 2.167 3.040 nonbonded pdb=" O ASN B 17 " pdb=" OG SER B 255 " model vdw 2.211 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 79 " model vdw 2.229 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" OE2 GLU L 81 " model vdw 2.231 3.120 nonbonded pdb=" OG SER L 12 " pdb=" OE2 GLU L 105 " model vdw 2.275 3.040 ... (remaining 29254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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 group one per residue 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: 23.190 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.500 Find NCS groups from input model: 0.020 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.006 0.043 4229 Z= 0.269 Angle : 0.826 7.155 5770 Z= 0.462 Chirality : 0.049 0.230 647 Planarity : 0.005 0.055 721 Dihedral : 12.526 68.971 1451 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.13 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.06 (0.38), residues: 196 loop : -3.05 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.021 0.002 TYR B 204 PHE 0.021 0.002 PHE B 59 TRP 0.017 0.002 TRP H 117 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 ( 4218) covalent geometry : angle 0.80236 / 0.46 ( 5741) SS BOND : bond 0.01351 / 0.65 ( 4) SS BOND : angle 3.12040 / 1.81 ( 8) hydrogen bonds : bond 0.19615 / 13.11 ( 109) hydrogen bonds : angle 7.26158 / 4.58 ( 303) link_BETA1-4 : bond 0.00037 / 0.02 ( 2) link_BETA1-4 : angle 2.55091 / 1.42 ( 6) link_NAG-ASN : bond 0.00342 / 0.18 ( 5) link_NAG-ASN : angle 2.87375 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.135 Fit side-chains REVERT: H 110 SER cc_start: 0.7742 (p) cc_final: 0.7538 (p) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0501 time to fit residues: 4.5479 Evaluate side-chains 58 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099899 restraints weight = 6359.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103348 restraints weight = 3404.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105597 restraints weight = 2265.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106850 restraints weight = 1737.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107885 restraints weight = 1476.846| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4229 Z= 0.144 Angle : 0.683 9.460 5770 Z= 0.344 Chirality : 0.044 0.213 647 Planarity : 0.004 0.046 721 Dihedral : 4.945 18.531 556 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.73 % Favored : 91.07 % Rotamer: Outliers : 1.79 % Allowed : 7.85 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.23 (0.37), residues: 207 loop : -2.96 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.016 0.002 TYR B 204 PHE 0.012 0.002 PHE H 80 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4218) covalent geometry : angle 0.66782 / 0.34 ( 5741) SS BOND : bond 0.00571 / 0.28 ( 4) SS BOND : angle 1.87581 / 1.05 ( 8) hydrogen bonds : bond 0.05793 / 3.89 ( 109) hydrogen bonds : angle 6.13402 / 3.96 ( 303) link_BETA1-4 : bond 0.00557 / 0.28 ( 2) link_BETA1-4 : angle 2.23896 / 1.28 ( 6) link_NAG-ASN : bond 0.00143 / 0.07 ( 5) link_NAG-ASN : angle 2.21904 / 1.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.128 Fit side-chains REVERT: B 97 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8037 (mtmm) REVERT: B 278 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7188 (ttpp) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.0443 time to fit residues: 4.3947 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 24 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.0670 chunk 31 optimal weight: 0.0170 overall best weight: 0.0446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103434 restraints weight = 6337.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106762 restraints weight = 3504.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108820 restraints weight = 2377.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110375 restraints weight = 1855.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111194 restraints weight = 1561.631| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4229 Z= 0.100 Angle : 0.619 9.470 5770 Z= 0.304 Chirality : 0.043 0.228 647 Planarity : 0.004 0.042 721 Dihedral : 4.600 20.678 556 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.57 % Allowed : 13.45 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.34 (0.37), residues: 209 loop : -2.88 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 99 TYR 0.016 0.001 TYR B 265 PHE 0.014 0.001 PHE B 133 TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 4218) covalent geometry : angle 0.59982 / 0.30 ( 5741) SS BOND : bond 0.00433 / 0.21 ( 4) SS BOND : angle 2.35948 / 1.36 ( 8) hydrogen bonds : bond 0.03910 / 2.60 ( 109) hydrogen bonds : angle 5.76691 / 3.75 ( 303) link_BETA1-4 : bond 0.00383 / 0.20 ( 2) link_BETA1-4 : angle 2.28757 / 1.31 ( 6) link_NAG-ASN : bond 0.00115 / 0.06 ( 5) link_NAG-ASN : angle 2.14474 / 1.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7985 (mtmm) REVERT: B 278 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7156 (ttpp) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.0655 time to fit residues: 5.0629 Evaluate side-chains 59 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098527 restraints weight = 6334.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101861 restraints weight = 3463.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103906 restraints weight = 2339.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105439 restraints weight = 1827.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106474 restraints weight = 1527.825| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4229 Z= 0.239 Angle : 0.736 9.534 5770 Z= 0.373 Chirality : 0.045 0.250 647 Planarity : 0.005 0.050 721 Dihedral : 5.200 21.782 556 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.91 % Allowed : 15.92 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.36 (0.37), residues: 205 loop : -2.95 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.024 0.002 TYR B 204 PHE 0.022 0.003 PHE B 59 TRP 0.008 0.002 TRP L 32 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 ( 4218) covalent geometry : angle 0.71430 / 0.37 ( 5741) SS BOND : bond 0.00809 / 0.40 ( 4) SS BOND : angle 3.42249 / 1.99 ( 8) hydrogen bonds : bond 0.07084 / 4.72 ( 109) hydrogen bonds : angle 5.96924 / 3.89 ( 303) link_BETA1-4 : bond 0.00462 / 0.23 ( 2) link_BETA1-4 : angle 1.87481 / 1.08 ( 6) link_NAG-ASN : bond 0.00221 / 0.12 ( 5) link_NAG-ASN : angle 2.28008 / 1.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8064 (mtmm) REVERT: B 278 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7193 (ttpp) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.0552 time to fit residues: 5.0547 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.1038 > 50:) chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 30 optimal weight: 0.3980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100433 restraints weight = 6296.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103762 restraints weight = 3457.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105994 restraints weight = 2344.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107227 restraints weight = 1812.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108325 restraints weight = 1546.865| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4229 Z= 0.132 Angle : 0.667 9.488 5770 Z= 0.331 Chirality : 0.044 0.246 647 Planarity : 0.004 0.045 721 Dihedral : 4.985 24.634 556 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.59 % Allowed : 17.04 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.45 (0.37), residues: 206 loop : -2.92 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 99 TYR 0.016 0.001 TYR B 265 PHE 0.019 0.002 PHE B 133 TRP 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4218) covalent geometry : angle 0.64320 / 0.32 ( 5741) SS BOND : bond 0.00492 / 0.24 ( 4) SS BOND : angle 3.50286 / 2.01 ( 8) hydrogen bonds : bond 0.05150 / 3.41 ( 109) hydrogen bonds : angle 5.74825 / 3.73 ( 303) link_BETA1-4 : bond 0.00376 / 0.19 ( 2) link_BETA1-4 : angle 1.96729 / 1.13 ( 6) link_NAG-ASN : bond 0.00076 / 0.04 ( 5) link_NAG-ASN : angle 2.20650 / 1.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8055 (mtmm) REVERT: B 278 LYS cc_start: 0.7704 (ttpp) cc_final: 0.7188 (ttpp) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.0595 time to fit residues: 5.5743 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 11 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102597 restraints weight = 6308.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105816 restraints weight = 3335.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107999 restraints weight = 2210.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109249 restraints weight = 1690.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110303 restraints weight = 1422.905| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4229 Z= 0.162 Angle : 0.700 9.499 5770 Z= 0.349 Chirality : 0.044 0.251 647 Planarity : 0.004 0.047 721 Dihedral : 5.130 29.014 556 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.59 % Allowed : 16.82 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.45 (0.37), residues: 206 loop : -2.92 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 78 TYR 0.017 0.001 TYR B 204 PHE 0.014 0.002 PHE B 59 TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4218) covalent geometry : angle 0.67295 / 0.34 ( 5741) SS BOND : bond 0.00606 / 0.30 ( 4) SS BOND : angle 4.12597 / 2.34 ( 8) hydrogen bonds : bond 0.05667 / 3.76 ( 109) hydrogen bonds : angle 5.75621 / 3.74 ( 303) link_BETA1-4 : bond 0.00490 / 0.24 ( 2) link_BETA1-4 : angle 1.86850 / 1.06 ( 6) link_NAG-ASN : bond 0.00115 / 0.06 ( 5) link_NAG-ASN : angle 2.21031 / 1.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.108 Fit side-chains REVERT: B 68 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7073 (mp) REVERT: B 274 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7497 (t) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.0424 time to fit residues: 3.7845 Evaluate side-chains 68 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.0000 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101038 restraints weight = 6291.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104247 restraints weight = 3343.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106705 restraints weight = 2250.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108222 restraints weight = 1716.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109151 restraints weight = 1428.066| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4229 Z= 0.171 Angle : 0.689 9.480 5770 Z= 0.348 Chirality : 0.044 0.250 647 Planarity : 0.004 0.047 721 Dihedral : 5.063 25.380 556 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.91 % Allowed : 17.49 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.50 (0.37), residues: 206 loop : -2.92 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.018 0.002 TYR B 204 PHE 0.015 0.002 PHE B 59 TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 4218) covalent geometry : angle 0.66986 / 0.34 ( 5741) SS BOND : bond 0.00499 / 0.25 ( 4) SS BOND : angle 2.82206 / 1.67 ( 8) hydrogen bonds : bond 0.05862 / 3.89 ( 109) hydrogen bonds : angle 5.77897 / 3.76 ( 303) link_BETA1-4 : bond 0.00444 / 0.22 ( 2) link_BETA1-4 : angle 1.87857 / 1.07 ( 6) link_NAG-ASN : bond 0.00106 / 0.05 ( 5) link_NAG-ASN : angle 2.22873 / 1.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.098 Fit side-chains REVERT: B 68 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7059 (mp) REVERT: B 274 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7508 (t) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.0454 time to fit residues: 4.1267 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099270 restraints weight = 6234.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102640 restraints weight = 3300.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104937 restraints weight = 2199.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106322 restraints weight = 1679.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107142 restraints weight = 1415.479| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 4229 Z= 0.257 Angle : 0.777 9.476 5770 Z= 0.395 Chirality : 0.047 0.252 647 Planarity : 0.005 0.051 721 Dihedral : 5.547 29.072 556 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 2.47 % Allowed : 18.39 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.51 (0.38), residues: 201 loop : -3.06 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.024 0.002 TYR B 204 PHE 0.023 0.003 PHE B 59 TRP 0.010 0.002 TRP L 32 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 ( 4218) covalent geometry : angle 0.75745 / 0.39 ( 5741) SS BOND : bond 0.00637 / 0.32 ( 4) SS BOND : angle 3.48602 / 2.07 ( 8) hydrogen bonds : bond 0.07292 / 4.85 ( 109) hydrogen bonds : angle 5.92892 / 3.88 ( 303) link_BETA1-4 : bond 0.00403 / 0.19 ( 2) link_BETA1-4 : angle 1.83275 / 1.05 ( 6) link_NAG-ASN : bond 0.00222 / 0.11 ( 5) link_NAG-ASN : angle 2.24455 / 1.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.108 Fit side-chains REVERT: B 68 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7094 (mp) REVERT: B 274 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7557 (t) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.0438 time to fit residues: 4.1039 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.0370 chunk 31 optimal weight: 0.0970 overall best weight: 0.1252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103598 restraints weight = 6337.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107079 restraints weight = 3356.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109258 restraints weight = 2210.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110968 restraints weight = 1689.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111819 restraints weight = 1392.883| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 4229 Z= 0.112 Angle : 0.672 9.441 5770 Z= 0.326 Chirality : 0.044 0.241 647 Planarity : 0.004 0.041 721 Dihedral : 4.970 28.032 556 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.02 % Allowed : 19.28 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.54 (0.37), residues: 207 loop : -2.98 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 99 TYR 0.017 0.001 TYR B 265 PHE 0.013 0.001 PHE H 80 TRP 0.009 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 4218) covalent geometry : angle 0.65521 / 0.32 ( 5741) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 2.51227 / 1.47 ( 8) hydrogen bonds : bond 0.04165 / 2.75 ( 109) hydrogen bonds : angle 5.60892 / 3.65 ( 303) link_BETA1-4 : bond 0.00438 / 0.22 ( 2) link_BETA1-4 : angle 2.03171 / 1.15 ( 6) link_NAG-ASN : bond 0.00135 / 0.07 ( 5) link_NAG-ASN : angle 2.04963 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7036 (mp) REVERT: B 97 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7981 (mtmm) REVERT: B 274 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7451 (t) REVERT: B 278 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7165 (ttpp) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.0637 time to fit residues: 5.4088 Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101864 restraints weight = 6190.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105129 restraints weight = 3294.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107259 restraints weight = 2175.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108484 restraints weight = 1659.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109436 restraints weight = 1396.404| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4229 Z= 0.185 Angle : 0.726 9.489 5770 Z= 0.361 Chirality : 0.045 0.248 647 Planarity : 0.004 0.043 721 Dihedral : 5.190 28.608 556 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.79 % Allowed : 19.51 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.52 (0.37), residues: 208 loop : -2.96 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.019 0.002 TYR B 204 PHE 0.015 0.002 PHE B 59 TRP 0.008 0.001 TRP L 32 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 4218) covalent geometry : angle 0.70752 / 0.36 ( 5741) SS BOND : bond 0.00524 / 0.26 ( 4) SS BOND : angle 2.99218 / 1.77 ( 8) hydrogen bonds : bond 0.06092 / 4.04 ( 109) hydrogen bonds : angle 5.73437 / 3.75 ( 303) link_BETA1-4 : bond 0.00468 / 0.23 ( 2) link_BETA1-4 : angle 1.92950 / 1.09 ( 6) link_NAG-ASN : bond 0.00124 / 0.06 ( 5) link_NAG-ASN : angle 2.16762 / 1.22 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.149 Fit side-chains REVERT: B 68 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7083 (mp) REVERT: B 274 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7491 (t) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0467 time to fit residues: 4.0046 Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 32 optimal weight: 0.0970 chunk 9 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.0000 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101548 restraints weight = 6228.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105037 restraints weight = 3328.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107341 restraints weight = 2200.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108675 restraints weight = 1672.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109833 restraints weight = 1410.207| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4229 Z= 0.147 Angle : 0.703 9.463 5770 Z= 0.345 Chirality : 0.044 0.246 647 Planarity : 0.004 0.043 721 Dihedral : 5.091 28.419 556 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 1.79 % Allowed : 20.18 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.56 (0.37), residues: 208 loop : -2.98 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 78 TYR 0.016 0.001 TYR B 265 PHE 0.013 0.002 PHE B 59 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4218) covalent geometry : angle 0.68624 / 0.34 ( 5741) SS BOND : bond 0.00429 / 0.21 ( 4) SS BOND : angle 2.71945 / 1.61 ( 8) hydrogen bonds : bond 0.05365 / 3.55 ( 109) hydrogen bonds : angle 5.66239 / 3.70 ( 303) link_BETA1-4 : bond 0.00434 / 0.21 ( 2) link_BETA1-4 : angle 1.95200 / 1.10 ( 6) link_NAG-ASN : bond 0.00086 / 0.05 ( 5) link_NAG-ASN : angle 2.09252 / 1.17 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1326.31 seconds wall clock time: 23 minutes 35.48 seconds (1415.48 seconds total)