Starting phenix.real_space_refine on Thu Mar 6 00:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_24402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_24402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_24402.map" model { file = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_24402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbu_24402/03_2025/7rbu_24402.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.17, per 1000 atoms: 1.99 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: 0.96 Conformation dependent library (CDL) restraints added in 463.6 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: 0.60 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: 1.06 Time building geometry restraints manager: 1.17 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: 105.720 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.460 ------------------------------------------------------------------------------- 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 4218 Z= 0.351 Angle : 0.802 6.189 5741 Z= 0.456 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 : 6.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (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 TRP 0.017 0.002 TRP H 117 HIS 0.004 0.001 HIS B 66 PHE 0.021 0.002 PHE B 59 TYR 0.021 0.002 TYR B 204 ARG 0.003 0.000 ARG L 61 *********************** 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 : 0.386 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: 0.1254 time to fit residues: 11.0625 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.0670 overall best weight: 0.1918 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.125288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100678 restraints weight = 6353.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103988 restraints weight = 3465.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106244 restraints weight = 2338.407| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4218 Z= 0.174 Angle : 0.657 9.382 5741 Z= 0.333 Chirality : 0.044 0.213 647 Planarity : 0.004 0.044 721 Dihedral : 7.915 56.056 703 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.13 % Favored : 91.67 % Rotamer: Outliers : 1.79 % Allowed : 8.07 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.24 (0.37), residues: 207 loop : -2.93 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.012 0.001 PHE H 80 TYR 0.015 0.001 TYR B 265 ARG 0.002 0.000 ARG L 61 *********************** 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 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.357 Fit side-chains REVERT: B 97 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8043 (mtmm) REVERT: B 278 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7169 (ttpp) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1218 time to fit residues: 11.5739 Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 0.0370 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 overall best weight: 0.1434 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.126585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101853 restraints weight = 6239.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105148 restraints weight = 3478.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107228 restraints weight = 2386.270| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4218 Z= 0.154 Angle : 0.614 9.566 5741 Z= 0.308 Chirality : 0.043 0.227 647 Planarity : 0.004 0.045 721 Dihedral : 7.339 55.966 703 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.24 % Allowed : 13.23 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.36 (0.37), residues: 207 loop : -2.90 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.016 0.001 PHE B 133 TYR 0.016 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 *********************** 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 68 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8333 (mtmt) cc_final: 0.8017 (mtmm) REVERT: B 278 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7174 (ttpp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1633 time to fit residues: 12.9631 Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 41 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099034 restraints weight = 6333.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102331 restraints weight = 3460.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104627 restraints weight = 2346.277| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4218 Z= 0.322 Angle : 0.695 9.589 5741 Z= 0.353 Chirality : 0.045 0.240 647 Planarity : 0.005 0.051 721 Dihedral : 7.144 56.380 703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.36 % Allowed : 15.70 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.37 (0.37), residues: 205 loop : -2.91 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS B 49 PHE 0.019 0.002 PHE B 133 TYR 0.021 0.002 TYR B 204 ARG 0.002 0.000 ARG B 78 *********************** 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 79 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8062 (mtmm) REVERT: B 278 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7184 (ttpp) outliers start: 15 outliers final: 8 residues processed: 68 average time/residue: 0.1371 time to fit residues: 12.4095 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 : 0.442 ------------------------------------------------------------------------------- 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 213 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.126164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101613 restraints weight = 6323.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105078 restraints weight = 3350.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107169 restraints weight = 2217.121| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4218 Z= 0.235 Angle : 0.659 9.535 5741 Z= 0.333 Chirality : 0.044 0.241 647 Planarity : 0.004 0.047 721 Dihedral : 6.744 55.904 703 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.04 % Allowed : 16.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.46 (0.37), residues: 205 loop : -2.90 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 PHE 0.021 0.002 PHE B 133 TYR 0.016 0.001 TYR B 265 ARG 0.001 0.000 ARG B 78 *********************** 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 80 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8063 (mtmm) REVERT: B 274 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7503 (t) REVERT: B 278 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7179 (ttpp) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.1177 time to fit residues: 11.6870 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.125817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101393 restraints weight = 6218.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.104757 restraints weight = 3308.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106823 restraints weight = 2213.084| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4218 Z= 0.239 Angle : 0.677 9.544 5741 Z= 0.341 Chirality : 0.044 0.244 647 Planarity : 0.004 0.047 721 Dihedral : 6.683 56.183 703 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.91 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.49 (0.37), residues: 207 loop : -2.91 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS B 49 PHE 0.014 0.002 PHE B 59 TYR 0.017 0.001 TYR B 204 ARG 0.001 0.000 ARG L 61 *********************** 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: 13 poor density : 58 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7053 (mp) REVERT: B 97 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8034 (mtmm) REVERT: B 113 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8038 (mttm) REVERT: B 274 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7494 (t) REVERT: B 278 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7176 (ttpp) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.1589 time to fit residues: 13.7754 Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.125191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100469 restraints weight = 6204.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103917 restraints weight = 3330.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106224 restraints weight = 2220.771| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4218 Z= 0.279 Angle : 0.690 9.530 5741 Z= 0.349 Chirality : 0.045 0.242 647 Planarity : 0.004 0.048 721 Dihedral : 6.623 56.307 703 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.69 % Allowed : 17.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.51 (0.37), residues: 206 loop : -2.93 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 49 PHE 0.017 0.002 PHE B 59 TYR 0.019 0.002 TYR B 204 ARG 0.002 0.000 ARG B 78 *********************** 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 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.426 Fit side-chains REVERT: B 68 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7058 (mp) REVERT: B 274 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7518 (t) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.1068 time to fit residues: 9.4541 Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 213 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.0270 chunk 8 optimal weight: 0.2980 chunk 26 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.0060 chunk 43 optimal weight: 0.0970 overall best weight: 0.1050 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.127280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103083 restraints weight = 6314.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106489 restraints weight = 3469.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108733 restraints weight = 2333.082| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 4218 Z= 0.144 Angle : 0.631 9.526 5741 Z= 0.307 Chirality : 0.043 0.236 647 Planarity : 0.004 0.040 721 Dihedral : 6.308 55.733 703 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.57 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.61 (0.37), residues: 207 loop : -2.92 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 PHE 0.012 0.001 PHE H 80 TYR 0.017 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 *********************** 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 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6997 (mp) REVERT: B 97 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7953 (mtmm) REVERT: B 113 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8020 (mttm) REVERT: B 278 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7139 (ttpp) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.1556 time to fit residues: 12.5613 Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 H residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099743 restraints weight = 6185.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102907 restraints weight = 3276.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.104990 restraints weight = 2166.332| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 4218 Z= 0.491 Angle : 0.803 9.548 5741 Z= 0.413 Chirality : 0.049 0.249 647 Planarity : 0.005 0.053 721 Dihedral : 6.949 57.133 703 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 2.24 % Allowed : 18.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.48 (0.38), residues: 201 loop : -3.08 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.003 0.001 HIS B 49 PHE 0.025 0.003 PHE B 59 TYR 0.025 0.002 TYR B 204 ARG 0.003 0.000 ARG L 61 *********************** 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 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.432 Fit side-chains REVERT: B 33 THR cc_start: 0.8117 (p) cc_final: 0.7813 (p) REVERT: B 68 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7094 (mp) REVERT: B 274 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7561 (t) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.1096 time to fit residues: 10.5361 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 overall best weight: 0.2698 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.125449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101131 restraints weight = 6296.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104585 restraints weight = 3335.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106911 restraints weight = 2202.852| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4218 Z= 0.220 Angle : 0.695 9.488 5741 Z= 0.345 Chirality : 0.045 0.236 647 Planarity : 0.004 0.044 721 Dihedral : 6.623 55.881 703 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.79 % Allowed : 19.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.49 (0.37), residues: 209 loop : -3.04 (0.29), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.014 0.002 PHE B 59 TYR 0.016 0.001 TYR B 265 ARG 0.001 0.000 ARG B 78 ********************** 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 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.403 Fit side-chains REVERT: B 68 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7028 (mp) REVERT: B 274 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7497 (t) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1025 time to fit residues: 9.1007 Evaluate side-chains 62 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain B residue 274 THR 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 0 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 44 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 43 optimal weight: 0.0060 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.1396 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105429 restraints weight = 6170.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108693 restraints weight = 3283.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110783 restraints weight = 2163.335| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4218 Z= 0.150 Angle : 0.657 9.530 5741 Z= 0.319 Chirality : 0.044 0.234 647 Planarity : 0.004 0.042 721 Dihedral : 6.371 55.975 703 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.57 % Allowed : 19.73 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.49 (0.37), residues: 213 loop : -2.94 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.012 0.001 PHE H 80 TYR 0.017 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.10 seconds wall clock time: 53 minutes 24.73 seconds (3204.73 seconds total)