Starting phenix.real_space_refine on Wed Sep 17 10:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmi_45749/09_2025/9cmi_45749.cif" } resolution = 2.83 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= 0.009 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 32 5.16 5 C 4991 2.51 5 N 1302 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7877 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2244 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain: "H" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "K" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.12, per 1000 atoms: 0.27 Number of scatterers: 7877 At special positions: 0 Unit cell: (78.565, 139.763, 148.033, 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 32 16.00 O 1552 8.00 N 1302 7.00 C 4991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 428.4 milliseconds Enol-peptide restraints added in 1.7 microseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 21 sheets defined 16.8% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.693A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.891A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.560A pdb=" N ASN B 173 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 4.281A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'H' and resid 242 through 244 No H-bonds generated for 'chain 'H' and resid 242 through 244' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.841A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 Processing helix chain 'L' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 86 removed outlier: 5.192A pdb=" N ILE B 83 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER B 154 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 143 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP B 152 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 141 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 154 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 139 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 41 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 63 removed outlier: 6.310A pdb=" N VAL B 57 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 134 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 208 removed outlier: 7.147A pdb=" N ALA B 205 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS B 241 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU B 207 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR B 243 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 297 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE B 261 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN B 276 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 263 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 227 Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33 removed outlier: 3.590A pdb=" N CYS H 48 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.589A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.589A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.784A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 190 through 194 removed outlier: 4.240A pdb=" N TYR H 234 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.637A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.951A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 11 removed outlier: 4.370A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AB9, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.797A pdb=" N LEU L 36 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.797A pdb=" N LEU L 36 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR L 122 " --> pdb=" O GLN L 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 139 through 143 removed outlier: 5.105A pdb=" N SER L 156 " --> pdb=" O LEU L 206 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU L 206 " --> pdb=" O SER L 156 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL L 158 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU L 204 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU L 160 " --> pdb=" O SER L 202 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER L 202 " --> pdb=" O LEU L 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN L 162 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 200 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 169 through 175 363 hydrogen bonds defined for protein. 972 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: 1.43 Time building geometry restraints manager: 0.85 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: 2499 1.34 - 1.46: 1890 1.46 - 1.58: 3612 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 8046 Sorted by residual: bond pdb=" N ASN B 222 " pdb=" CA ASN B 222 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 8.11e+00 bond pdb=" N SER L 119 " pdb=" CA SER L 119 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.00e-02 1.00e+04 7.57e+00 bond pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta sigma weight residual 1.452 1.491 -0.039 1.41e-02 5.03e+03 7.47e+00 bond pdb=" N SER B 217 " pdb=" CA SER B 217 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.91e+00 bond pdb=" N SER L 117 " pdb=" CA SER L 117 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.70e+00 ... (remaining 8041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.38: 10934 6.38 - 12.77: 1 12.77 - 19.15: 0 19.15 - 25.53: 3 25.53 - 31.92: 3 Bond angle restraints: 10941 Sorted by residual: angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.52 78.60 31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBR AV0 H 301 " ideal model delta sigma weight residual 107.79 80.57 27.22 3.00e+00 1.11e-01 8.23e+01 angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 110.70 84.18 26.52 3.00e+00 1.11e-01 7.81e+01 angle pdb=" CBS AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 105.72 80.46 25.26 3.00e+00 1.11e-01 7.09e+01 angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.98 133.27 -22.29 3.00e+00 1.11e-01 5.52e+01 ... (remaining 10936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 4525 22.25 - 44.50: 246 44.50 - 66.75: 34 66.75 - 89.00: 18 89.00 - 111.25: 9 Dihedral angle restraints: 4832 sinusoidal: 1886 harmonic: 2946 Sorted by residual: dihedral pdb=" OAS AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAU AV0 H 301 " ideal model delta sinusoidal sigma weight residual 59.49 170.74 -111.25 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CCN AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAU AV0 H 301 " ideal model delta sinusoidal sigma weight residual 178.46 -70.35 -111.19 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CCR AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAS AV0 H 301 " ideal model delta sinusoidal sigma weight residual 174.22 63.24 110.98 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 4829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 727 0.030 - 0.059: 343 0.059 - 0.089: 110 0.089 - 0.118: 65 0.118 - 0.148: 9 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL A 56 " pdb=" N VAL A 56 " pdb=" C VAL A 56 " pdb=" CB VAL A 56 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE L 46 " pdb=" N ILE L 46 " pdb=" C ILE L 46 " pdb=" CB ILE L 46 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1251 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 188 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO H 189 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C VAL B 272 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS B 273 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 68 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO L 69 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 69 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 69 " 0.021 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 499 2.73 - 3.27: 7674 3.27 - 3.82: 13236 3.82 - 4.36: 16040 4.36 - 4.90: 28038 Nonbonded interactions: 65487 Sorted by model distance: nonbonded pdb=" OD2 ASP H 141 " pdb=" OH TYR L 61 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASP B 292 " pdb=" OH TYR B 296 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OE2 GLU B 184 " model vdw 2.229 3.040 nonbonded pdb=" OG SER L 39 " pdb=" OD2 ASP L 42 " model vdw 2.247 3.040 nonbonded pdb=" NH1 ARG B 143 " pdb=" OD2 ASP B 151 " model vdw 2.251 3.120 ... (remaining 65482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.003 0.042 8052 Z= 0.180 Angle : 0.822 31.916 10953 Z= 0.383 Chirality : 0.042 0.148 1254 Planarity : 0.004 0.043 1373 Dihedral : 15.697 111.252 2936 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 1.04 % Allowed : 9.15 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.87 (0.26), residues: 1015 helix: 1.94 (0.42), residues: 156 sheet: -0.67 (0.25), residues: 409 loop : -1.32 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 113 TYR 0.010 0.001 TYR L 111 PHE 0.014 0.001 PHE B 316 TRP 0.015 0.001 TRP H 125 HIS 0.004 0.001 HIS H 61 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8046) covalent geometry : angle 0.82246 (10941) SS BOND : bond 0.00381 ( 6) SS BOND : angle 0.61152 ( 12) hydrogen bonds : bond 0.08011 ( 344) hydrogen bonds : angle 6.10760 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8443 (ptp) cc_final: 0.8214 (mtp) REVERT: A 146 ASP cc_start: 0.7780 (t70) cc_final: 0.7574 (t0) REVERT: B 97 GLN cc_start: 0.8816 (tt0) cc_final: 0.8576 (tt0) REVERT: B 110 GLU cc_start: 0.8485 (tp30) cc_final: 0.8268 (tm-30) REVERT: B 234 TRP cc_start: 0.8432 (p-90) cc_final: 0.8014 (p-90) REVERT: H 54 ASN cc_start: 0.7471 (t0) cc_final: 0.7100 (p0) REVERT: H 102 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8908 (mmpt) REVERT: H 115 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8495 (mp0) REVERT: H 241 LYS cc_start: 0.8086 (tptp) cc_final: 0.7823 (tppt) REVERT: K 31 ARG cc_start: 0.8378 (mmp-170) cc_final: 0.8064 (mmp80) REVERT: K 95 TYR cc_start: 0.7842 (m-80) cc_final: 0.7274 (m-80) REVERT: L 192 ASP cc_start: 0.7732 (t0) cc_final: 0.7448 (t0) outliers start: 9 outliers final: 3 residues processed: 143 average time/residue: 0.5350 time to fit residues: 81.1817 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain H residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN L 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.120179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088033 restraints weight = 15618.569| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.49 r_work: 0.3423 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8052 Z= 0.121 Angle : 0.830 31.595 10953 Z= 0.353 Chirality : 0.042 0.171 1254 Planarity : 0.004 0.042 1373 Dihedral : 8.644 92.514 1231 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.01 % Allowed : 15.18 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.65 (0.26), residues: 1015 helix: 2.12 (0.43), residues: 155 sheet: -0.54 (0.25), residues: 414 loop : -1.19 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 113 TYR 0.012 0.001 TYR B 133 PHE 0.014 0.001 PHE K 37 TRP 0.011 0.001 TRP H 125 HIS 0.006 0.001 HIS H 61 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8046) covalent geometry : angle 0.82997 (10941) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.46793 ( 12) hydrogen bonds : bond 0.03008 ( 344) hydrogen bonds : angle 5.45328 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.7777 (t70) cc_final: 0.7481 (t0) REVERT: B 126 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 234 TRP cc_start: 0.8511 (p-90) cc_final: 0.8106 (p-90) REVERT: H 54 ASN cc_start: 0.7410 (t0) cc_final: 0.7081 (p0) REVERT: H 102 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8885 (mmmt) REVERT: H 115 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8638 (mp0) REVERT: H 241 LYS cc_start: 0.8104 (tptp) cc_final: 0.7821 (tppt) REVERT: K 19 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7916 (mmt90) REVERT: K 31 ARG cc_start: 0.8311 (mmp-170) cc_final: 0.8012 (mmp80) REVERT: K 34 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: K 83 MET cc_start: 0.9274 (mtp) cc_final: 0.8997 (mtp) REVERT: K 95 TYR cc_start: 0.8048 (m-80) cc_final: 0.7477 (m-80) outliers start: 26 outliers final: 8 residues processed: 119 average time/residue: 0.5015 time to fit residues: 63.8029 Evaluate side-chains 97 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN H 61 HIS ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.119823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087013 restraints weight = 15549.027| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.53 r_work: 0.3371 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8052 Z= 0.172 Angle : 0.830 31.618 10953 Z= 0.357 Chirality : 0.042 0.174 1254 Planarity : 0.004 0.043 1373 Dihedral : 7.611 96.667 1229 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.24 % Allowed : 17.27 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.63 (0.26), residues: 1015 helix: 1.94 (0.42), residues: 155 sheet: -0.49 (0.26), residues: 416 loop : -1.13 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 113 TYR 0.011 0.001 TYR B 133 PHE 0.015 0.001 PHE B 316 TRP 0.018 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8046) covalent geometry : angle 0.82999 (10941) SS BOND : bond 0.00403 ( 6) SS BOND : angle 0.63315 ( 12) hydrogen bonds : bond 0.03123 ( 344) hydrogen bonds : angle 5.50634 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6955 (OUTLIER) cc_final: 0.6691 (p) REVERT: B 126 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 234 TRP cc_start: 0.8564 (p-90) cc_final: 0.8183 (p-90) REVERT: H 54 ASN cc_start: 0.7462 (t0) cc_final: 0.7105 (p0) REVERT: H 102 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8855 (mmmt) REVERT: H 115 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8721 (mp0) REVERT: H 241 LYS cc_start: 0.8094 (tptp) cc_final: 0.7804 (tppt) REVERT: H 252 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7977 (tm-30) REVERT: K 31 ARG cc_start: 0.8355 (mmp-170) cc_final: 0.8060 (mmp80) REVERT: K 34 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: K 83 MET cc_start: 0.9313 (mtp) cc_final: 0.9040 (mtp) REVERT: K 95 TYR cc_start: 0.8059 (m-80) cc_final: 0.7504 (m-80) REVERT: L 168 GLU cc_start: 0.8268 (mp0) cc_final: 0.7173 (pp20) outliers start: 28 outliers final: 14 residues processed: 109 average time/residue: 0.5616 time to fit residues: 65.2467 Evaluate side-chains 99 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086927 restraints weight = 15944.417| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.55 r_work: 0.3396 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8052 Z= 0.134 Angle : 0.822 31.499 10953 Z= 0.348 Chirality : 0.042 0.178 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.393 97.292 1229 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.36 % Allowed : 19.00 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.52 (0.27), residues: 1015 helix: 2.01 (0.42), residues: 155 sheet: -0.36 (0.26), residues: 417 loop : -1.12 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 113 TYR 0.016 0.001 TYR K 32 PHE 0.013 0.001 PHE B 316 TRP 0.013 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8046) covalent geometry : angle 0.82185 (10941) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.56763 ( 12) hydrogen bonds : bond 0.02929 ( 344) hydrogen bonds : angle 5.32352 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6516 (p) REVERT: B 126 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: B 234 TRP cc_start: 0.8548 (p-90) cc_final: 0.8183 (p-90) REVERT: B 263 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7993 (mp) REVERT: H 54 ASN cc_start: 0.7453 (t0) cc_final: 0.7147 (p0) REVERT: H 69 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7737 (ptmm) REVERT: H 102 LYS cc_start: 0.9144 (mmpt) cc_final: 0.8845 (mmmt) REVERT: H 115 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8721 (mp0) REVERT: H 241 LYS cc_start: 0.8100 (tptp) cc_final: 0.7813 (tppt) REVERT: K 19 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7993 (tpp-160) REVERT: K 31 ARG cc_start: 0.8354 (mmp-170) cc_final: 0.8063 (mmp80) REVERT: K 34 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: K 83 MET cc_start: 0.9295 (mtp) cc_final: 0.9037 (mtp) REVERT: K 95 TYR cc_start: 0.8061 (m-80) cc_final: 0.7527 (m-80) REVERT: L 29 MET cc_start: 0.7297 (mmm) cc_final: 0.7056 (mtp) REVERT: L 168 GLU cc_start: 0.8265 (mp0) cc_final: 0.7207 (pp20) outliers start: 29 outliers final: 14 residues processed: 109 average time/residue: 0.4930 time to fit residues: 57.6855 Evaluate side-chains 108 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 3 optimal weight: 0.0170 chunk 38 optimal weight: 0.5980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.119370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086879 restraints weight = 15754.689| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.55 r_work: 0.3412 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8052 Z= 0.128 Angle : 0.825 31.513 10953 Z= 0.347 Chirality : 0.041 0.177 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.279 97.453 1229 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.59 % Allowed : 19.70 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.43 (0.27), residues: 1015 helix: 2.08 (0.42), residues: 155 sheet: -0.27 (0.27), residues: 417 loop : -1.09 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 113 TYR 0.009 0.001 TYR K 32 PHE 0.014 0.001 PHE B 316 TRP 0.013 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8046) covalent geometry : angle 0.82573 (10941) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.52459 ( 12) hydrogen bonds : bond 0.02912 ( 344) hydrogen bonds : angle 5.27024 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7147 (mt) cc_final: 0.6872 (mp) REVERT: B 126 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 234 TRP cc_start: 0.8539 (p-90) cc_final: 0.8195 (p-90) REVERT: B 263 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7956 (mp) REVERT: H 54 ASN cc_start: 0.7436 (t0) cc_final: 0.7116 (p0) REVERT: H 102 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8843 (mmmt) REVERT: H 115 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8759 (mp0) REVERT: H 241 LYS cc_start: 0.8098 (tptp) cc_final: 0.7814 (tppt) REVERT: K 19 ARG cc_start: 0.8319 (mmt90) cc_final: 0.8010 (tpp-160) REVERT: K 31 ARG cc_start: 0.8356 (mmp-170) cc_final: 0.8117 (mmm-85) REVERT: K 34 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7836 (mtp) REVERT: K 83 MET cc_start: 0.9307 (mtp) cc_final: 0.9104 (mtp) REVERT: K 95 TYR cc_start: 0.8046 (m-80) cc_final: 0.7476 (m-80) REVERT: K 110 TYR cc_start: 0.8844 (m-80) cc_final: 0.8622 (m-80) REVERT: L 42 ASP cc_start: 0.8276 (t0) cc_final: 0.7921 (t0) REVERT: L 114 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: L 168 GLU cc_start: 0.8282 (mp0) cc_final: 0.7275 (pp20) outliers start: 31 outliers final: 17 residues processed: 110 average time/residue: 0.4935 time to fit residues: 58.2575 Evaluate side-chains 104 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 HIS ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.119600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.087441 restraints weight = 15738.316| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.54 r_work: 0.3420 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8052 Z= 0.122 Angle : 0.824 31.277 10953 Z= 0.346 Chirality : 0.041 0.178 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.213 97.792 1229 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.13 % Allowed : 21.09 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.33 (0.27), residues: 1015 helix: 2.10 (0.42), residues: 155 sheet: -0.12 (0.27), residues: 409 loop : -1.11 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 113 TYR 0.011 0.001 TYR B 133 PHE 0.014 0.001 PHE B 316 TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8046) covalent geometry : angle 0.82398 (10941) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.46688 ( 12) hydrogen bonds : bond 0.02894 ( 344) hydrogen bonds : angle 5.16965 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6742 (OUTLIER) cc_final: 0.6446 (p) REVERT: A 126 LEU cc_start: 0.7162 (mt) cc_final: 0.6838 (mp) REVERT: B 126 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 234 TRP cc_start: 0.8543 (p-90) cc_final: 0.8197 (p-90) REVERT: H 54 ASN cc_start: 0.7432 (t0) cc_final: 0.6898 (p0) REVERT: H 57 SER cc_start: 0.8853 (t) cc_final: 0.8346 (m) REVERT: H 69 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7715 (ptmm) REVERT: H 102 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8936 (mmpt) REVERT: H 115 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8752 (mp0) REVERT: H 241 LYS cc_start: 0.8080 (tptp) cc_final: 0.7797 (tppt) REVERT: K 19 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7896 (tpp-160) REVERT: K 31 ARG cc_start: 0.8319 (mmp-170) cc_final: 0.8101 (mmm-85) REVERT: K 34 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8269 (mtp) REVERT: K 83 MET cc_start: 0.9310 (mtp) cc_final: 0.9080 (mtp) REVERT: K 95 TYR cc_start: 0.8044 (m-80) cc_final: 0.7468 (m-80) REVERT: L 42 ASP cc_start: 0.8316 (t0) cc_final: 0.7961 (t0) REVERT: L 114 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6515 (pt0) REVERT: L 168 GLU cc_start: 0.8289 (mp0) cc_final: 0.7289 (pp20) outliers start: 27 outliers final: 16 residues processed: 112 average time/residue: 0.5168 time to fit residues: 61.8989 Evaluate side-chains 105 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 HIS ** 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 = 0.4125 r_free = 0.4125 target = 0.118909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.086628 restraints weight = 15940.779| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.52 r_work: 0.3428 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8052 Z= 0.121 Angle : 0.831 31.280 10953 Z= 0.351 Chirality : 0.041 0.182 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.179 97.931 1229 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.55 % Allowed : 21.90 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.28 (0.27), residues: 1015 helix: 2.13 (0.42), residues: 155 sheet: -0.01 (0.27), residues: 404 loop : -1.14 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 113 TYR 0.009 0.001 TYR B 133 PHE 0.014 0.001 PHE B 316 TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8046) covalent geometry : angle 0.83092 (10941) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.44011 ( 12) hydrogen bonds : bond 0.02861 ( 344) hydrogen bonds : angle 5.10684 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 105 THR cc_start: 0.6763 (OUTLIER) cc_final: 0.6452 (p) REVERT: A 126 LEU cc_start: 0.7355 (mt) cc_final: 0.6871 (mp) REVERT: B 126 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 234 TRP cc_start: 0.8484 (p-90) cc_final: 0.8165 (p-90) REVERT: H 54 ASN cc_start: 0.7405 (t0) cc_final: 0.7125 (p0) REVERT: H 69 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7734 (ptmm) REVERT: H 102 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8775 (mmmt) REVERT: H 115 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8818 (mp0) REVERT: H 241 LYS cc_start: 0.8053 (tptp) cc_final: 0.7778 (tppt) REVERT: K 19 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7878 (tpp-160) REVERT: K 31 ARG cc_start: 0.8280 (mmp-170) cc_final: 0.8062 (mmm-85) REVERT: K 34 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: K 83 MET cc_start: 0.9317 (mtp) cc_final: 0.9090 (mtp) REVERT: K 95 TYR cc_start: 0.8040 (m-80) cc_final: 0.7444 (m-80) REVERT: L 42 ASP cc_start: 0.8349 (t0) cc_final: 0.8016 (t0) REVERT: L 114 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: L 168 GLU cc_start: 0.8276 (mp0) cc_final: 0.7361 (pp20) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 0.4765 time to fit residues: 52.8346 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.1980 chunk 31 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.084545 restraints weight = 16023.112| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.50 r_work: 0.3406 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8052 Z= 0.147 Angle : 0.838 31.315 10953 Z= 0.356 Chirality : 0.042 0.186 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.213 98.711 1229 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.43 % Allowed : 22.25 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.32 (0.27), residues: 1015 helix: 2.05 (0.42), residues: 155 sheet: -0.08 (0.27), residues: 412 loop : -1.12 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 113 TYR 0.019 0.001 TYR H 59 PHE 0.014 0.001 PHE B 316 TRP 0.016 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8046) covalent geometry : angle 0.83859 (10941) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.50930 ( 12) hydrogen bonds : bond 0.02960 ( 344) hydrogen bonds : angle 5.18632 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6526 (p) REVERT: A 126 LEU cc_start: 0.7394 (mt) cc_final: 0.7030 (mp) REVERT: A 131 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7405 (tmt) REVERT: B 126 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 234 TRP cc_start: 0.8507 (p-90) cc_final: 0.8185 (p-90) REVERT: H 54 ASN cc_start: 0.7386 (t0) cc_final: 0.6907 (p0) REVERT: H 57 SER cc_start: 0.8880 (t) cc_final: 0.8431 (m) REVERT: H 102 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8786 (mmmt) REVERT: H 115 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8756 (mp0) REVERT: H 241 LYS cc_start: 0.8042 (tptp) cc_final: 0.7768 (tppt) REVERT: K 19 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7827 (tpp-160) REVERT: K 20 LEU cc_start: 0.8461 (mm) cc_final: 0.8219 (mm) REVERT: K 34 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: K 83 MET cc_start: 0.9316 (mtp) cc_final: 0.9023 (mtp) REVERT: K 95 TYR cc_start: 0.8037 (m-80) cc_final: 0.7435 (m-80) REVERT: L 42 ASP cc_start: 0.8339 (t0) cc_final: 0.8012 (t0) REVERT: L 114 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: L 192 ASP cc_start: 0.7790 (t0) cc_final: 0.7586 (t0) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.5450 time to fit residues: 58.2971 Evaluate side-chains 102 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.3980 chunk 46 optimal weight: 0.0270 chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.120027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.087414 restraints weight = 16199.071| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.56 r_work: 0.3471 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8052 Z= 0.114 Angle : 0.827 31.247 10953 Z= 0.351 Chirality : 0.041 0.183 1254 Planarity : 0.004 0.040 1373 Dihedral : 7.113 97.691 1229 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.55 % Allowed : 22.02 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.20 (0.27), residues: 1015 helix: 2.16 (0.43), residues: 155 sheet: 0.07 (0.28), residues: 403 loop : -1.10 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 113 TYR 0.009 0.001 TYR H 86 PHE 0.013 0.001 PHE B 316 TRP 0.010 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8046) covalent geometry : angle 0.82747 (10941) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.42293 ( 12) hydrogen bonds : bond 0.02786 ( 344) hydrogen bonds : angle 5.03189 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6505 (p) REVERT: A 126 LEU cc_start: 0.7420 (mt) cc_final: 0.6913 (mp) REVERT: A 131 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7811 (tmt) REVERT: B 126 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 234 TRP cc_start: 0.8423 (p-90) cc_final: 0.8124 (p-90) REVERT: H 54 ASN cc_start: 0.7362 (t0) cc_final: 0.6919 (p0) REVERT: H 57 SER cc_start: 0.8625 (t) cc_final: 0.8160 (m) REVERT: H 102 LYS cc_start: 0.9095 (mmpt) cc_final: 0.8810 (mmmt) REVERT: H 115 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8831 (mp0) REVERT: H 169 LYS cc_start: 0.7422 (pptt) cc_final: 0.7203 (pmtt) REVERT: H 241 LYS cc_start: 0.7999 (tptp) cc_final: 0.7741 (tppt) REVERT: K 19 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7773 (tpp-160) REVERT: K 20 LEU cc_start: 0.8418 (mm) cc_final: 0.8152 (mm) REVERT: K 34 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: K 95 TYR cc_start: 0.8028 (m-80) cc_final: 0.7421 (m-80) REVERT: L 42 ASP cc_start: 0.8355 (t0) cc_final: 0.8038 (t0) REVERT: L 114 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: L 168 GLU cc_start: 0.8392 (mp0) cc_final: 0.7450 (pp20) REVERT: L 180 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8517 (mp10) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 0.5271 time to fit residues: 59.1098 Evaluate side-chains 101 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.119556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.087089 restraints weight = 16091.254| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.57 r_work: 0.3469 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8052 Z= 0.123 Angle : 0.849 31.264 10953 Z= 0.362 Chirality : 0.042 0.181 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.094 97.963 1229 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.09 % Allowed : 22.71 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.21 (0.27), residues: 1015 helix: 2.16 (0.42), residues: 155 sheet: 0.10 (0.28), residues: 398 loop : -1.14 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 31 TYR 0.010 0.001 TYR H 59 PHE 0.013 0.001 PHE B 316 TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8046) covalent geometry : angle 0.84948 (10941) SS BOND : bond 0.00234 ( 6) SS BOND : angle 0.43548 ( 12) hydrogen bonds : bond 0.02809 ( 344) hydrogen bonds : angle 5.03408 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6267 (p) REVERT: A 126 LEU cc_start: 0.7452 (mt) cc_final: 0.6936 (mp) REVERT: A 131 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7756 (tmt) REVERT: B 126 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 234 TRP cc_start: 0.8415 (p-90) cc_final: 0.8121 (p-90) REVERT: H 54 ASN cc_start: 0.7361 (t0) cc_final: 0.6906 (p0) REVERT: H 57 SER cc_start: 0.8585 (t) cc_final: 0.8150 (m) REVERT: H 102 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8728 (mmmt) REVERT: H 115 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8825 (mp0) REVERT: H 169 LYS cc_start: 0.7396 (pptt) cc_final: 0.7131 (pmtt) REVERT: H 241 LYS cc_start: 0.7984 (tptp) cc_final: 0.7724 (tppt) REVERT: K 20 LEU cc_start: 0.8428 (mm) cc_final: 0.8216 (mm) REVERT: K 34 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7565 (ttm) REVERT: K 95 TYR cc_start: 0.8022 (m-80) cc_final: 0.7411 (m-80) REVERT: L 42 ASP cc_start: 0.8357 (t0) cc_final: 0.8050 (t0) REVERT: L 114 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6599 (pt0) REVERT: L 168 GLU cc_start: 0.8386 (mp0) cc_final: 0.7463 (pp20) REVERT: L 180 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8537 (mp10) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.5123 time to fit residues: 54.8206 Evaluate side-chains 103 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.118316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085458 restraints weight = 15982.959| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.56 r_work: 0.3422 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8052 Z= 0.135 Angle : 0.848 31.157 10953 Z= 0.363 Chirality : 0.042 0.181 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.055 98.651 1229 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.43 % Allowed : 22.13 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.16 (0.27), residues: 1015 helix: 2.17 (0.43), residues: 155 sheet: 0.15 (0.28), residues: 393 loop : -1.12 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 113 TYR 0.014 0.001 TYR H 59 PHE 0.014 0.001 PHE B 316 TRP 0.014 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8046) covalent geometry : angle 0.84819 (10941) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.45646 ( 12) hydrogen bonds : bond 0.02851 ( 344) hydrogen bonds : angle 5.06366 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.14 seconds wall clock time: 68 minutes 13.57 seconds (4093.57 seconds total)