Starting phenix.real_space_refine on Tue Mar 3 12:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rbu_24402/03_2026/7rbu_24402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbu_24402/03_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_24402/03_2026/7rbu_24402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2026/7rbu_24402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2026/7rbu_24402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2026/7rbu_24402.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.01, per 1000 atoms: 0.25 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: 0.38 Conformation dependent library (CDL) restraints added in 180.4 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: 0.17 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: 0.58 Time building geometry restraints manager: 0.50 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: 2315 17.16 - 34.32: 178 34.32 - 51.48: 45 51.48 - 68.64: 10 68.64 - 85.80: 2 Dihedral angle restraints: 2550 sinusoidal: 1072 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 2547 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: 21.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 12.814 68.971 1598 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 covalent geometry : bond 0.00555 ( 4218) covalent geometry : angle 0.80236 ( 5741) SS BOND : bond 0.01351 ( 4) SS BOND : angle 3.12040 ( 8) hydrogen bonds : bond 0.19615 ( 109) hydrogen bonds : angle 7.26158 ( 303) link_BETA1-4 : bond 0.00037 ( 2) link_BETA1-4 : angle 2.55091 ( 6) link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 2.87375 ( 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 : 0.162 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: 0.0541 time to fit residues: 4.8383 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 : 0.153 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100091 restraints weight = 6355.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103347 restraints weight = 3480.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105541 restraints weight = 2355.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106762 restraints weight = 1825.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107730 restraints weight = 1560.613| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4229 Z= 0.144 Angle : 0.690 9.475 5770 Z= 0.347 Chirality : 0.044 0.213 647 Planarity : 0.004 0.046 721 Dihedral : 7.947 55.976 703 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.09 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: 0.24 (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 0.001 TYR B 204 PHE 0.013 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 covalent geometry : bond 0.00324 ( 4218) covalent geometry : angle 0.67312 ( 5741) SS BOND : bond 0.00569 ( 4) SS BOND : angle 1.89607 ( 8) hydrogen bonds : bond 0.05845 ( 109) hydrogen bonds : angle 6.16445 ( 303) link_BETA1-4 : bond 0.00497 ( 2) link_BETA1-4 : angle 2.28964 ( 6) link_NAG-ASN : bond 0.00130 ( 5) link_NAG-ASN : angle 2.38049 ( 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 : 0.114 Fit side-chains REVERT: B 97 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8045 (mtmm) REVERT: B 278 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7186 (ttpp) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.0521 time to fit residues: 5.1783 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 : 0.142 ------------------------------------------------------------------------------- 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: 0.0970 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098985 restraints weight = 6375.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102276 restraints weight = 3520.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104435 restraints weight = 2401.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105625 restraints weight = 1867.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106638 restraints weight = 1602.365| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4229 Z= 0.179 Angle : 0.699 9.563 5770 Z= 0.353 Chirality : 0.045 0.231 647 Planarity : 0.005 0.051 721 Dihedral : 7.840 58.925 703 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.47 % Allowed : 14.35 % Favored : 83.18 % 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: -2.20 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.33 (0.37), residues: 206 loop : -3.01 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 78 TYR 0.020 0.002 TYR B 204 PHE 0.016 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 covalent geometry : bond 0.00425 ( 4218) covalent geometry : angle 0.67854 ( 5741) SS BOND : bond 0.00606 ( 4) SS BOND : angle 2.68092 ( 8) hydrogen bonds : bond 0.06301 ( 109) hydrogen bonds : angle 6.02478 ( 303) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 1.90881 ( 6) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 2.49900 ( 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 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 83 VAL cc_start: 0.8256 (t) cc_final: 0.7970 (p) REVERT: B 278 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7201 (ttpp) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.0586 time to fit residues: 5.1789 Evaluate side-chains 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 115 GLN 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 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: 0.1980 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 0.0870 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101605 restraints weight = 6289.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104764 restraints weight = 3492.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106983 restraints weight = 2409.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108273 restraints weight = 1885.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109182 restraints weight = 1607.048| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4229 Z= 0.113 Angle : 0.645 9.573 5770 Z= 0.316 Chirality : 0.043 0.233 647 Planarity : 0.004 0.044 721 Dihedral : 6.935 55.552 703 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.69 % Allowed : 15.47 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.08 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.44 (0.37), residues: 207 loop : -2.96 (0.30), residues: 297 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 0.018 0.001 PHE B 133 TRP 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4218) covalent geometry : angle 0.62236 ( 5741) SS BOND : bond 0.00814 ( 4) SS BOND : angle 2.85054 ( 8) hydrogen bonds : bond 0.04543 ( 109) hydrogen bonds : angle 5.77000 ( 303) link_BETA1-4 : bond 0.00496 ( 2) link_BETA1-4 : angle 1.94813 ( 6) link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 2.40114 ( 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 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 VAL cc_start: 0.8210 (t) cc_final: 0.8007 (p) REVERT: B 97 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8053 (mtmm) REVERT: B 278 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7175 (ttpp) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.0565 time to fit residues: 5.0885 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 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 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100618 restraints weight = 6290.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103957 restraints weight = 3435.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106206 restraints weight = 2322.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107499 restraints weight = 1793.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108360 restraints weight = 1522.976| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1391 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= 0.145 Angle : 0.675 9.557 5770 Z= 0.334 Chirality : 0.044 0.240 647 Planarity : 0.004 0.046 721 Dihedral : 6.732 55.998 703 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.69 % Allowed : 17.26 % Favored : 80.04 % 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: -2.01 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.48 (0.37), residues: 205 loop : -2.89 (0.30), residues: 299 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 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4218) covalent geometry : angle 0.64959 ( 5741) SS BOND : bond 0.00504 ( 4) SS BOND : angle 3.48204 ( 8) hydrogen bonds : bond 0.05403 ( 109) hydrogen bonds : angle 5.72270 ( 303) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 1.88210 ( 6) link_NAG-ASN : bond 0.00106 ( 5) link_NAG-ASN : angle 2.39259 ( 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 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 83 VAL cc_start: 0.8253 (t) cc_final: 0.8013 (p) REVERT: B 97 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8116 (mtmm) REVERT: B 274 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7487 (t) REVERT: B 278 LYS cc_start: 0.7705 (ttpp) cc_final: 0.7160 (ttpp) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.0617 time to fit residues: 5.5135 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100178 restraints weight = 6451.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103523 restraints weight = 3515.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105753 restraints weight = 2372.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107093 restraints weight = 1828.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108165 restraints weight = 1550.258| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4229 Z= 0.150 Angle : 0.685 9.567 5770 Z= 0.340 Chirality : 0.044 0.244 647 Planarity : 0.004 0.045 721 Dihedral : 6.595 56.103 703 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.04 % Allowed : 16.14 % Favored : 79.82 % 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: -1.98 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.51 (0.37), residues: 207 loop : -2.89 (0.30), residues: 297 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 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4218) covalent geometry : angle 0.65635 ( 5741) SS BOND : bond 0.00593 ( 4) SS BOND : angle 4.04385 ( 8) hydrogen bonds : bond 0.05479 ( 109) hydrogen bonds : angle 5.69560 ( 303) link_BETA1-4 : bond 0.00542 ( 2) link_BETA1-4 : angle 1.90089 ( 6) link_NAG-ASN : bond 0.00100 ( 5) link_NAG-ASN : angle 2.38365 ( 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 81 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7051 (mp) REVERT: B 83 VAL cc_start: 0.8246 (t) cc_final: 0.7999 (p) REVERT: B 97 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8134 (mtmm) REVERT: B 113 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8014 (mttm) REVERT: B 274 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 278 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7177 (ttpp) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 0.0592 time to fit residues: 5.8435 Evaluate side-chains 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 78 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.099628 restraints weight = 6327.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103077 restraints weight = 3341.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105356 restraints weight = 2214.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106798 restraints weight = 1688.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107616 restraints weight = 1417.579| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 4229 Z= 0.232 Angle : 0.771 9.527 5770 Z= 0.388 Chirality : 0.046 0.245 647 Planarity : 0.005 0.049 721 Dihedral : 6.824 56.681 703 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 2.91 % Allowed : 17.26 % Favored : 79.82 % 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: -2.12 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.45 (0.38), residues: 206 loop : -3.01 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.023 0.002 TYR B 204 PHE 0.022 0.002 PHE B 59 TRP 0.009 0.002 TRP B 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 4218) covalent geometry : angle 0.74761 ( 5741) SS BOND : bond 0.00519 ( 4) SS BOND : angle 3.59669 ( 8) hydrogen bonds : bond 0.06995 ( 109) hydrogen bonds : angle 5.90537 ( 303) link_BETA1-4 : bond 0.00409 ( 2) link_BETA1-4 : angle 1.82268 ( 6) link_NAG-ASN : bond 0.00239 ( 5) link_NAG-ASN : angle 2.55988 ( 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 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.142 Fit side-chains REVERT: B 68 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7072 (mp) REVERT: B 274 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7547 (t) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.0428 time to fit residues: 4.0134 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 110 SER Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101898 restraints weight = 6183.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105342 restraints weight = 3295.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107715 restraints weight = 2188.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109008 restraints weight = 1664.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109906 restraints weight = 1408.609| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4229 Z= 0.143 Angle : 0.693 9.530 5770 Z= 0.343 Chirality : 0.044 0.237 647 Planarity : 0.004 0.043 721 Dihedral : 6.574 55.866 703 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.69 % Allowed : 17.49 % Favored : 79.82 % 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: 0.54 (0.37), residues: 206 loop : -2.97 (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 265 PHE 0.012 0.002 PHE H 80 TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4218) covalent geometry : angle 0.67261 ( 5741) SS BOND : bond 0.00439 ( 4) SS BOND : angle 2.74670 ( 8) hydrogen bonds : bond 0.05207 ( 109) hydrogen bonds : angle 5.69719 ( 303) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 1.97300 ( 6) link_NAG-ASN : bond 0.00089 ( 5) link_NAG-ASN : angle 2.39847 ( 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 72 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7045 (mp) REVERT: B 83 VAL cc_start: 0.8251 (t) cc_final: 0.8004 (p) REVERT: B 97 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8110 (mtmm) REVERT: B 113 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8048 (mttm) REVERT: B 274 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7498 (t) REVERT: B 278 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7166 (ttpp) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.0605 time to fit residues: 5.3111 Evaluate side-chains 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 L residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.0020 overall best weight: 0.2346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102006 restraints weight = 6309.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105523 restraints weight = 3314.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107672 restraints weight = 2180.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109290 restraints weight = 1673.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110443 restraints weight = 1378.860| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1731 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= 0.133 Angle : 0.677 9.534 5770 Z= 0.333 Chirality : 0.044 0.238 647 Planarity : 0.004 0.044 721 Dihedral : 6.439 56.065 703 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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: -2.04 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.56 (0.37), residues: 209 loop : -3.04 (0.29), residues: 295 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 0.012 0.001 PHE H 80 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4218) covalent geometry : angle 0.65794 ( 5741) SS BOND : bond 0.00440 ( 4) SS BOND : angle 2.61386 ( 8) hydrogen bonds : bond 0.05072 ( 109) hydrogen bonds : angle 5.61236 ( 303) link_BETA1-4 : bond 0.00489 ( 2) link_BETA1-4 : angle 1.98159 ( 6) link_NAG-ASN : bond 0.00098 ( 5) link_NAG-ASN : angle 2.37642 ( 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 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.146 Fit side-chains REVERT: B 68 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7035 (mp) REVERT: B 83 VAL cc_start: 0.8242 (t) cc_final: 0.8003 (p) REVERT: B 274 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7468 (t) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0476 time to fit residues: 4.0425 Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100740 restraints weight = 6190.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104164 restraints weight = 3297.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106282 restraints weight = 2193.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107874 restraints weight = 1693.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108935 restraints weight = 1403.546| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4229 Z= 0.184 Angle : 0.718 9.537 5770 Z= 0.359 Chirality : 0.045 0.238 647 Planarity : 0.004 0.047 721 Dihedral : 6.591 56.305 703 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -2.07 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.60 (0.38), residues: 203 loop : -3.03 (0.29), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 78 TYR 0.019 0.002 TYR B 204 PHE 0.016 0.002 PHE B 59 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 4218) covalent geometry : angle 0.69838 ( 5741) SS BOND : bond 0.00538 ( 4) SS BOND : angle 2.89342 ( 8) hydrogen bonds : bond 0.06119 ( 109) hydrogen bonds : angle 5.69262 ( 303) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 1.91491 ( 6) link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 2.42857 ( 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 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.162 Fit side-chains REVERT: B 68 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7066 (mp) REVERT: B 274 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7516 (t) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.0399 time to fit residues: 3.6340 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101297 restraints weight = 6229.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104513 restraints weight = 3287.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106695 restraints weight = 2173.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108117 restraints weight = 1648.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108818 restraints weight = 1372.257| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4229 Z= 0.201 Angle : 0.743 9.521 5770 Z= 0.371 Chirality : 0.045 0.240 647 Planarity : 0.005 0.047 721 Dihedral : 6.710 56.313 703 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.69 % Allowed : 18.39 % Favored : 78.92 % 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: 0.56 (0.38), residues: 205 loop : -3.02 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.020 0.002 TYR B 204 PHE 0.018 0.002 PHE B 59 TRP 0.008 0.002 TRP B 104 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 4218) covalent geometry : angle 0.72341 ( 5741) SS BOND : bond 0.00605 ( 4) SS BOND : angle 2.97029 ( 8) hydrogen bonds : bond 0.06433 ( 109) hydrogen bonds : angle 5.74913 ( 303) link_BETA1-4 : bond 0.00441 ( 2) link_BETA1-4 : angle 1.88119 ( 6) link_NAG-ASN : bond 0.00147 ( 5) link_NAG-ASN : angle 2.46655 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.88 seconds wall clock time: 22 minutes 26.58 seconds (1346.58 seconds total)