Starting phenix.real_space_refine on Wed Feb 12 13:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmi_45749/02_2025/9cmi_45749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmi_45749/02_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_45749/02_2025/9cmi_45749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmi_45749/02_2025/9cmi_45749.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmi_45749/02_2025/9cmi_45749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmi_45749/02_2025/9cmi_45749.cif" } resolution = 2.83 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= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.55, per 1000 atoms: 0.70 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: 2.21 Conformation dependent library (CDL) restraints added in 867.9 milliseconds 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: 1.04 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: 2.42 Time building geometry restraints manager: 2.48 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: 2.540 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.410 Find NCS groups from input model: 0.070 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- 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 8046 Z= 0.217 Angle : 0.822 31.916 10941 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 : 8.96 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 (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: -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 TRP 0.015 0.001 TRP H 125 HIS 0.004 0.001 HIS H 61 PHE 0.014 0.001 PHE B 316 TYR 0.010 0.001 TYR L 111 ARG 0.002 0.000 ARG H 113 *********************** 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 : 0.905 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: 1.1228 time to fit residues: 170.7291 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 : 0.912 ------------------------------------------------------------------------------- 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 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087582 restraints weight = 15490.933| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.49 r_work: 0.3409 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8046 Z= 0.192 Angle : 0.833 31.655 10941 Z= 0.356 Chirality : 0.042 0.168 1254 Planarity : 0.004 0.042 1373 Dihedral : 8.201 93.065 1231 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 15.41 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.69 (0.26), residues: 1015 helix: 2.09 (0.43), residues: 155 sheet: -0.55 (0.25), residues: 414 loop : -1.21 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 125 HIS 0.006 0.001 HIS H 61 PHE 0.014 0.001 PHE K 37 TYR 0.012 0.001 TYR B 133 ARG 0.008 0.001 ARG H 113 *********************** 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 128 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8847 (tt0) cc_final: 0.8627 (tt0) REVERT: B 126 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: B 234 TRP cc_start: 0.8526 (p-90) cc_final: 0.8127 (p-90) REVERT: H 54 ASN cc_start: 0.7415 (t0) cc_final: 0.7090 (p0) REVERT: H 102 LYS cc_start: 0.9190 (mmpt) cc_final: 0.8880 (mmmt) REVERT: H 115 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8643 (mp0) REVERT: H 241 LYS cc_start: 0.8085 (tptp) cc_final: 0.7796 (tppt) REVERT: K 31 ARG cc_start: 0.8320 (mmp-170) cc_final: 0.8018 (mmp80) REVERT: K 34 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8097 (mtp) REVERT: K 83 MET cc_start: 0.9286 (mtp) cc_final: 0.9007 (mtp) REVERT: K 95 TYR cc_start: 0.8063 (m-80) cc_final: 0.7518 (m-80) REVERT: L 168 GLU cc_start: 0.8205 (mp0) cc_final: 0.7071 (pp20) outliers start: 26 outliers final: 9 residues processed: 117 average time/residue: 1.1402 time to fit residues: 142.3098 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 47 THR 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 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 78 GLN H 61 HIS ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.118506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085949 restraints weight = 15826.930| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.53 r_work: 0.3385 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8046 Z= 0.228 Angle : 0.823 31.625 10941 Z= 0.353 Chirality : 0.042 0.173 1254 Planarity : 0.004 0.043 1373 Dihedral : 7.568 96.647 1229 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.13 % Allowed : 17.27 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.61 (0.26), residues: 1015 helix: 1.99 (0.42), residues: 155 sheet: -0.46 (0.26), residues: 416 loop : -1.14 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 125 HIS 0.004 0.001 HIS H 61 PHE 0.014 0.001 PHE B 316 TYR 0.012 0.001 TYR K 32 ARG 0.009 0.000 ARG H 113 *********************** 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 123 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6519 (p) REVERT: B 97 GLN cc_start: 0.8853 (tt0) cc_final: 0.8628 (tt0) REVERT: B 126 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: B 234 TRP cc_start: 0.8558 (p-90) cc_final: 0.8181 (p-90) REVERT: B 263 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 284 ASP cc_start: 0.9025 (m-30) cc_final: 0.8825 (m-30) REVERT: H 54 ASN cc_start: 0.7503 (t0) cc_final: 0.7158 (p0) REVERT: H 102 LYS cc_start: 0.9163 (mmpt) cc_final: 0.8856 (mmmt) REVERT: H 115 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8696 (mp0) REVERT: H 241 LYS cc_start: 0.8084 (tptp) cc_final: 0.7795 (tppt) REVERT: H 252 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7962 (tm-30) REVERT: K 19 ARG cc_start: 0.8266 (mmt90) cc_final: 0.7953 (tpp-160) REVERT: K 20 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8150 (mm) REVERT: K 31 ARG cc_start: 0.8341 (mmp-170) cc_final: 0.8045 (mmp80) REVERT: K 34 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8379 (mtp) REVERT: K 83 MET cc_start: 0.9304 (mtp) cc_final: 0.9081 (mtp) REVERT: K 95 TYR cc_start: 0.8067 (m-80) cc_final: 0.7496 (m-80) REVERT: L 29 MET cc_start: 0.7392 (mmm) cc_final: 0.6784 (mpp) REVERT: L 168 GLU cc_start: 0.8278 (mp0) cc_final: 0.7173 (pp20) outliers start: 27 outliers final: 11 residues processed: 111 average time/residue: 1.1250 time to fit residues: 133.3948 Evaluate side-chains 101 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 20 LEU 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 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 80 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 64 optimal weight: 0.0060 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 78 GLN H 211 GLN K 39 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084447 restraints weight = 15797.054| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.56 r_work: 0.3359 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8046 Z= 0.278 Angle : 0.847 31.672 10941 Z= 0.364 Chirality : 0.043 0.179 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.714 96.947 1229 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.71 % Allowed : 19.00 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.72 (0.26), residues: 1015 helix: 1.76 (0.42), residues: 155 sheet: -0.49 (0.26), residues: 419 loop : -1.21 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 PHE 0.015 0.001 PHE B 316 TYR 0.018 0.001 TYR H 59 ARG 0.009 0.000 ARG H 113 *********************** 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 123 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6541 (p) REVERT: B 126 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: B 234 TRP cc_start: 0.8583 (p-90) cc_final: 0.8212 (p-90) REVERT: B 284 ASP cc_start: 0.9035 (m-30) cc_final: 0.8819 (m-30) REVERT: H 54 ASN cc_start: 0.7524 (t0) cc_final: 0.7139 (p0) REVERT: H 102 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8848 (mmmt) REVERT: H 115 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8718 (mp0) REVERT: H 241 LYS cc_start: 0.8105 (tptp) cc_final: 0.7809 (tppt) REVERT: K 19 ARG cc_start: 0.8277 (mmt90) cc_final: 0.8068 (tpp-160) REVERT: K 31 ARG cc_start: 0.8408 (mmp-170) cc_final: 0.8109 (mmp80) REVERT: K 34 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: K 95 TYR cc_start: 0.8065 (m-80) cc_final: 0.7509 (m-80) REVERT: L 29 MET cc_start: 0.7346 (mmm) cc_final: 0.7120 (mtp) outliers start: 32 outliers final: 14 residues processed: 109 average time/residue: 1.0510 time to fit residues: 123.0193 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 292 ASP 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 42 ASP Chi-restraints excluded: chain L residue 140 VAL 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 99 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** L 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.086577 restraints weight = 15591.798| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.57 r_work: 0.3401 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8046 Z= 0.188 Angle : 0.831 31.689 10941 Z= 0.350 Chirality : 0.042 0.177 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.640 95.906 1229 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.82 % Allowed : 19.81 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.50 (0.27), residues: 1015 helix: 1.98 (0.42), residues: 155 sheet: -0.33 (0.26), residues: 415 loop : -1.10 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.014 0.001 PHE B 316 TYR 0.009 0.001 TYR B 133 ARG 0.009 0.000 ARG H 113 *********************** 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 124 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6636 (p) REVERT: B 126 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 234 TRP cc_start: 0.8545 (p-90) cc_final: 0.8185 (p-90) REVERT: B 263 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7950 (mp) REVERT: H 54 ASN cc_start: 0.7490 (t0) cc_final: 0.6887 (p0) REVERT: H 57 SER cc_start: 0.9056 (t) cc_final: 0.8554 (m) REVERT: H 102 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8832 (mmmt) REVERT: H 115 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8698 (mp0) REVERT: H 241 LYS cc_start: 0.8101 (tptp) cc_final: 0.7811 (tppt) REVERT: K 19 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8065 (tpp-160) REVERT: K 31 ARG cc_start: 0.8404 (mmp-170) cc_final: 0.8159 (mmm-85) REVERT: K 34 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7856 (mtp) REVERT: K 95 TYR cc_start: 0.8042 (m-80) cc_final: 0.7480 (m-80) REVERT: L 42 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7778 (t0) REVERT: L 114 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6584 (pt0) REVERT: L 168 GLU cc_start: 0.8411 (mp0) cc_final: 0.7299 (pp20) outliers start: 33 outliers final: 15 residues processed: 111 average time/residue: 1.0366 time to fit residues: 123.4349 Evaluate side-chains 103 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 42 ASP 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 83 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 70 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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** L 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.118292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085786 restraints weight = 15634.748| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.53 r_work: 0.3386 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8046 Z= 0.227 Angle : 0.845 31.619 10941 Z= 0.360 Chirality : 0.042 0.181 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.340 99.556 1229 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.59 % Allowed : 20.74 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.51 (0.26), residues: 1015 helix: 1.88 (0.42), residues: 155 sheet: -0.27 (0.27), residues: 411 loop : -1.14 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 PHE 0.015 0.001 PHE B 316 TYR 0.011 0.001 TYR B 133 ARG 0.011 0.001 ARG H 113 *********************** 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 118 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6891 (OUTLIER) cc_final: 0.6617 (p) REVERT: A 131 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7481 (tmt) REVERT: B 126 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 234 TRP cc_start: 0.8522 (p-90) cc_final: 0.8182 (p-90) REVERT: B 263 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7962 (mp) REVERT: H 54 ASN cc_start: 0.7498 (t0) cc_final: 0.7151 (p0) REVERT: H 102 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8844 (mmmt) REVERT: H 115 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8732 (mp0) REVERT: H 241 LYS cc_start: 0.8103 (tptp) cc_final: 0.7814 (tppt) REVERT: K 19 ARG cc_start: 0.8282 (mmt90) cc_final: 0.8005 (tpp-160) REVERT: K 31 ARG cc_start: 0.8373 (mmp-170) cc_final: 0.8138 (mmm-85) REVERT: K 34 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: K 95 TYR cc_start: 0.8039 (m-80) cc_final: 0.7456 (m-80) REVERT: L 42 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7784 (t0) REVERT: L 114 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: L 168 GLU cc_start: 0.8423 (mp0) cc_final: 0.7373 (pp20) REVERT: L 192 ASP cc_start: 0.7838 (t0) cc_final: 0.7581 (t0) outliers start: 31 outliers final: 14 residues processed: 108 average time/residue: 1.1424 time to fit residues: 131.6692 Evaluate side-chains 103 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 42 ASP 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 50 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** L 214 HIS ** 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 = 0.4200 r_free = 0.4200 target = 0.130130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097131 restraints weight = 15750.941| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.67 r_work: 0.3457 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8046 Z= 0.164 Angle : 0.832 31.360 10941 Z= 0.351 Chirality : 0.041 0.173 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.146 97.090 1229 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.13 % Allowed : 21.55 % 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 (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: -0.32 (0.27), residues: 1015 helix: 2.09 (0.42), residues: 155 sheet: -0.06 (0.27), residues: 400 loop : -1.13 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 132 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.009 0.001 TYR B 133 ARG 0.010 0.000 ARG H 113 *********************** 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 122 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7714 (ttt) REVERT: B 126 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 234 TRP cc_start: 0.8444 (p-90) cc_final: 0.8159 (p-90) REVERT: H 54 ASN cc_start: 0.7410 (t0) cc_final: 0.6916 (p0) REVERT: H 57 SER cc_start: 0.8794 (t) cc_final: 0.8360 (m) REVERT: H 69 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7738 (ptmm) REVERT: H 115 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8854 (mp0) REVERT: H 241 LYS cc_start: 0.7997 (tptp) cc_final: 0.7737 (tppt) REVERT: K 31 ARG cc_start: 0.8263 (mmp-170) cc_final: 0.8061 (mmm-85) REVERT: K 34 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: K 95 TYR cc_start: 0.8040 (m-80) cc_final: 0.7418 (m-80) REVERT: L 42 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7871 (t0) REVERT: L 114 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6575 (pt0) REVERT: L 168 GLU cc_start: 0.8433 (mp0) cc_final: 0.7469 (pp20) REVERT: L 180 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8088 (mp-120) outliers start: 27 outliers final: 14 residues processed: 113 average time/residue: 1.0863 time to fit residues: 131.7182 Evaluate side-chains 99 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 132 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 42 ASP 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 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.117119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.085108 restraints weight = 15956.950| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.48 r_work: 0.3413 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8046 Z= 0.206 Angle : 0.854 31.467 10941 Z= 0.363 Chirality : 0.042 0.187 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.118 98.090 1229 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.55 % Allowed : 22.13 % 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 (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: -0.35 (0.26), residues: 1015 helix: 1.95 (0.42), residues: 155 sheet: -0.03 (0.27), residues: 403 loop : -1.16 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.010 0.001 TYR B 133 ARG 0.010 0.001 ARG H 113 *********************** 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: 22 poor density : 83 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: B 234 TRP cc_start: 0.8493 (p-90) cc_final: 0.8184 (p-90) REVERT: H 54 ASN cc_start: 0.7457 (t0) cc_final: 0.6920 (p0) REVERT: H 57 SER cc_start: 0.8799 (t) cc_final: 0.8335 (m) REVERT: H 115 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8773 (mp0) REVERT: K 31 ARG cc_start: 0.8237 (mmp-170) cc_final: 0.8036 (mmm-85) REVERT: K 34 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: K 95 TYR cc_start: 0.8026 (m-80) cc_final: 0.7412 (m-80) REVERT: L 42 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7839 (t0) REVERT: L 114 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6677 (pt0) REVERT: L 168 GLU cc_start: 0.8433 (mp0) cc_final: 0.7305 (pp20) REVERT: L 180 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8518 (mp10) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 1.0417 time to fit residues: 109.8533 Evaluate side-chains 97 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 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 42 ASP 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 15 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5548 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.119223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.086946 restraints weight = 15975.345| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.54 r_work: 0.3434 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8046 Z= 0.181 Angle : 0.854 31.364 10941 Z= 0.362 Chirality : 0.042 0.182 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.098 98.535 1229 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 21.67 % 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 (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: -0.24 (0.26), residues: 1015 helix: 2.06 (0.42), residues: 155 sheet: 0.17 (0.28), residues: 387 loop : -1.19 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.022 0.001 TYR H 59 ARG 0.010 0.000 ARG H 113 *********************** 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 106 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7428 (tpp) cc_final: 0.7217 (ttt) REVERT: B 126 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 234 TRP cc_start: 0.8454 (p-90) cc_final: 0.8134 (p-90) REVERT: H 54 ASN cc_start: 0.7445 (t0) cc_final: 0.6895 (p0) REVERT: H 57 SER cc_start: 0.8661 (t) cc_final: 0.8209 (m) REVERT: H 115 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8771 (mp0) REVERT: K 34 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: K 83 MET cc_start: 0.8494 (mtm) cc_final: 0.8013 (mtm) REVERT: K 95 TYR cc_start: 0.8041 (m-80) cc_final: 0.7425 (m-80) REVERT: L 42 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7843 (t0) REVERT: L 114 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: L 168 GLU cc_start: 0.8440 (mp0) cc_final: 0.7327 (pp20) REVERT: L 180 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8502 (mp10) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 1.1058 time to fit residues: 115.9573 Evaluate side-chains 96 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 ASP 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 97 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 99 optimal weight: 0.0070 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6202 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.119427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.087018 restraints weight = 16136.456| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.55 r_work: 0.3463 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8046 Z= 0.191 Angle : 0.863 31.382 10941 Z= 0.366 Chirality : 0.042 0.182 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.077 98.044 1229 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (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: -0.28 (0.26), residues: 1015 helix: 1.95 (0.41), residues: 155 sheet: 0.08 (0.27), residues: 401 loop : -1.15 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.014 0.001 PHE B 316 TYR 0.022 0.001 TYR H 59 ARG 0.010 0.001 ARG H 113 ********************** 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 100 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7505 (tpp) cc_final: 0.7264 (ttt) REVERT: A 131 MET cc_start: 0.8161 (tmt) cc_final: 0.7596 (tmt) REVERT: B 126 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 234 TRP cc_start: 0.8403 (p-90) cc_final: 0.8120 (p-90) REVERT: H 54 ASN cc_start: 0.7353 (t0) cc_final: 0.6895 (p0) REVERT: H 57 SER cc_start: 0.8686 (t) cc_final: 0.8217 (m) REVERT: H 115 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8827 (mp0) REVERT: K 34 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8078 (mtp) REVERT: K 83 MET cc_start: 0.8565 (mtm) cc_final: 0.8123 (mtm) REVERT: K 95 TYR cc_start: 0.8021 (m-80) cc_final: 0.7391 (m-80) REVERT: L 42 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7880 (t0) REVERT: L 114 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6619 (pt0) REVERT: L 168 GLU cc_start: 0.8429 (mp0) cc_final: 0.7383 (pp20) REVERT: L 180 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8520 (mp10) outliers start: 18 outliers final: 14 residues processed: 95 average time/residue: 1.0356 time to fit residues: 105.8642 Evaluate side-chains 97 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN 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 42 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 56 optimal weight: 0.0270 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.0040 chunk 73 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 overall best weight: 0.2828 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.132827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099983 restraints weight = 15712.965| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.73 r_work: 0.3496 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8046 Z= 0.161 Angle : 0.852 31.328 10941 Z= 0.362 Chirality : 0.042 0.179 1254 Planarity : 0.004 0.050 1373 Dihedral : 6.978 96.829 1229 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.55 % Allowed : 22.25 % 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 (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: -0.11 (0.27), residues: 1015 helix: 2.06 (0.42), residues: 155 sheet: 0.19 (0.27), residues: 401 loop : -1.04 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 132 HIS 0.003 0.001 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.008 0.001 TYR B 133 ARG 0.011 0.001 ARG K 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7488.43 seconds wall clock time: 132 minutes 42.98 seconds (7962.98 seconds total)