Starting phenix.real_space_refine on Sun Aug 24 15:11:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dq0_27645/08_2025/8dq0_27645.map" } resolution = 3.74 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= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4750 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 52 5.16 5 C 5494 2.51 5 N 1567 2.21 5 O 1569 1.98 5 H 8445 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17129 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3807 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "D" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3778 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "A" Number of atoms: 4758 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 4741 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Conformer: "B" Number of residues, atoms: 298, 4741 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} bond proxies already assigned to first conformer: 4777 Chain: "B" Number of atoms: 4746 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 4738 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Conformer: "B" Number of residues, atoms: 298, 4738 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} bond proxies already assigned to first conformer: 4784 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'K5G': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'K5G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.25 Number of scatterers: 17129 At special positions: 0 Unit cell: (73.53, 104.49, 130.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 52 16.00 O 1569 8.00 N 1567 7.00 C 5494 6.00 H 8445 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.15 Conformation dependent library (CDL) restraints added in 615.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 51.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.271A pdb=" N VAL C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 4.334A pdb=" N GLY C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.425A pdb=" N GLN C 103 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.205A pdb=" N TRP C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 170 removed outlier: 4.489A pdb=" N GLU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 208 through 224 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.702A pdb=" N ALA C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 23 through 38 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 77 through 80 Processing helix chain 'D' and resid 81 through 90 removed outlier: 4.282A pdb=" N GLY D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.965A pdb=" N TRP D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 169 removed outlier: 4.459A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.513A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.675A pdb=" N ALA D 231 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.571A pdb=" N ALA A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.523A pdb=" N GLN A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.820A pdb=" N VAL A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 232 through 255 Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.608A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.065A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.581A pdb=" N ALA B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 232 through 255 removed outlier: 3.577A pdb=" N TYR B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.872A pdb=" N LEU B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.864A pdb=" N GLY B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.674A pdb=" N THR C 63 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C 43 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 94 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.937A pdb=" N TYR D 43 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 11 removed outlier: 6.518A pdb=" N LEU A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TRP A 34 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP A 65 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 36 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS A 63 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 91 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TRP A 65 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N SER A 93 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 6.703A pdb=" N HIS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 166 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 174 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.976A pdb=" N TRP B 34 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LEU B 66 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 36 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU B 91 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP B 65 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 155 removed outlier: 10.039A pdb=" N VAL B 164 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY B 177 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 174 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 182 431 hydrogen bonds defined for protein. 1238 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: 3.38 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 8420 1.04 - 1.27: 1469 1.27 - 1.49: 3748 1.49 - 1.72: 3614 1.72 - 1.94: 83 Bond restraints: 17334 Sorted by residual: bond pdb=" C12 K5G D 301 " pdb=" C13 K5G D 301 " ideal model delta sigma weight residual 1.520 1.875 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" C12 K5G C 301 " pdb=" C13 K5G C 301 " ideal model delta sigma weight residual 1.520 1.871 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C12 K5G C 301 " pdb=" C16 K5G C 301 " ideal model delta sigma weight residual 1.531 1.397 0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C12 K5G D 301 " pdb=" C16 K5G D 301 " ideal model delta sigma weight residual 1.531 1.403 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C12 K5G D 301 " pdb=" N11 K5G D 301 " ideal model delta sigma weight residual 1.429 1.318 0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 17329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.37: 31198 7.37 - 14.74: 10 14.74 - 22.11: 0 22.11 - 29.48: 0 29.48 - 36.85: 1 Bond angle restraints: 31209 Sorted by residual: angle pdb=" C09 K5G D 301 " pdb=" N11 K5G D 301 " pdb=" C12 K5G D 301 " ideal model delta sigma weight residual 123.28 160.13 -36.85 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N LEU D 69 " pdb=" CA LEU D 69 " pdb=" C LEU D 69 " ideal model delta sigma weight residual 111.07 104.45 6.62 1.07e+00 8.73e-01 3.82e+01 angle pdb=" N SER B 33 " pdb=" CA SER B 33 " pdb=" C SER B 33 " ideal model delta sigma weight residual 110.48 119.37 -8.89 1.48e+00 4.57e-01 3.61e+01 angle pdb=" O PHE B 195 " pdb=" C PHE B 195 " pdb=" N ASP B 196 " ideal model delta sigma weight residual 122.19 117.04 5.15 1.03e+00 9.43e-01 2.50e+01 angle pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N ASP B 196 " ideal model delta sigma weight residual 119.07 124.52 -5.45 1.20e+00 6.94e-01 2.06e+01 ... (remaining 31204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 7596 27.04 - 54.08: 431 54.08 - 81.12: 66 81.12 - 108.16: 7 108.16 - 135.20: 1 Dihedral angle restraints: 8101 sinusoidal: 4436 harmonic: 3665 Sorted by residual: dihedral pdb=" CA THR A 68 " pdb=" C THR A 68 " pdb=" N HIS A 69 " pdb=" CA HIS A 69 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY B 39 " pdb=" C GLY B 39 " pdb=" N GLY B 40 " pdb=" CA GLY B 40 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLU C 92 " pdb=" C GLU C 92 " pdb=" N MET C 93 " pdb=" CA MET C 93 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 8098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1204 0.090 - 0.180: 90 0.180 - 0.271: 6 0.271 - 0.361: 1 0.361 - 0.451: 1 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA GLU B 31 " pdb=" N GLU B 31 " pdb=" C GLU B 31 " pdb=" CB GLU B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C12 K5G D 301 " pdb=" C13 K5G D 301 " pdb=" C16 K5G D 301 " pdb=" N11 K5G D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA SER B 33 " pdb=" N SER B 33 " pdb=" C SER B 33 " pdb=" CB SER B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1299 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " 0.024 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" N ASP B 196 " -0.074 2.00e-02 2.50e+03 pdb=" CA ASP B 196 " 0.018 2.00e-02 2.50e+03 pdb=" H ASP B 196 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 55 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C 56 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 31 " 0.021 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" N ALA B 32 " -0.068 2.00e-02 2.50e+03 pdb=" CA ALA B 32 " 0.017 2.00e-02 2.50e+03 pdb=" H ALA B 32 " 0.030 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.28: 2740 2.28 - 2.89: 39610 2.89 - 3.49: 48690 3.49 - 4.10: 66271 4.10 - 4.70: 103358 Nonbonded interactions: 260669 Sorted by model distance: nonbonded pdb="HH22 ARG B 28 " pdb=" OE1 GLU B 31 " model vdw 1.680 2.450 nonbonded pdb=" HE1 TRP A 250 " pdb=" O GLU B 185 " model vdw 1.716 2.450 nonbonded pdb=" O ARG A 148 " pdb="HH12 ARG A 171 " model vdw 1.743 2.450 nonbonded pdb=" HE1 TRP C 11 " pdb=" OE1 GLU D 149 " model vdw 1.752 2.450 nonbonded pdb=" HG SER B 93 " pdb="HG13 VAL B 164 " model vdw 1.752 2.270 ... (remaining 260664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB or name OG )) or resid 34 through 59 or resid 61 through 1 \ 96 or resid 198 through 244 or resid 246 through 254 or (resid 255 and (name N o \ r name CA or name C or name O )) or resid 256 through 298)) selection = (chain 'B' and (resid 1 through 59 or resid 61 through 196 or resid 198 through \ 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 through 244 or resid 246 through 298)) } ncs_group { reference = (chain 'C' and (resid 4 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or resid 51 through 191 or (resi \ d 192 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or resid 193 through 211 or (resid 212 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or resid 213 through 301)) selection = (chain 'D' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2)) or (resid 10 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resi \ d 11 through 301)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.100 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.008 0.355 8889 Z= 0.422 Angle : 0.981 36.852 12057 Z= 0.503 Chirality : 0.050 0.451 1302 Planarity : 0.006 0.101 1565 Dihedral : 16.037 135.204 3321 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.20 % Allowed : 0.43 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1070 helix: 0.17 (0.23), residues: 458 sheet: -2.39 (0.37), residues: 162 loop : -1.67 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 107 TYR 0.032 0.003 TYR C 72 PHE 0.014 0.002 PHE D 101 TRP 0.012 0.001 TRP B 269 HIS 0.011 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00844 ( 8889) covalent geometry : angle 0.98109 (12057) hydrogen bonds : bond 0.16524 ( 431) hydrogen bonds : angle 6.65636 ( 1238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.484 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: symmetry clash revert: symmetry clash REVERT: C 63 THR cc_start: 0.8113 (p) cc_final: 0.7608 (t) REVERT: C 234 TYR cc_start: 0.8518 (m-10) cc_final: 0.8171 (m-10) REVERT: D 58 THR cc_start: 0.8310 (m) cc_final: 0.8072 (m) REVERT: D 109 ASN cc_start: 0.7251 (m-40) cc_final: 0.6727 (m-40) REVERT: A 31 GLU cc_start: 0.7700 (tp30) cc_final: 0.7495 (tp30) REVERT: A 236 SER cc_start: 0.9067 (m) cc_final: 0.8860 (m) REVERT: B 31 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: B 170 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8036 (ttm110) outliers start: 11 outliers final: 5 residues processed: 229 average time/residue: 0.2235 time to fit residues: 66.9506 Evaluate side-chains 210 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 170 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN B 9 GLN B 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.131083 restraints weight = 44916.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.136935 restraints weight = 16351.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.140553 restraints weight = 8079.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.142874 restraints weight = 4890.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.144150 restraints weight = 3473.633| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8889 Z= 0.127 Angle : 0.556 5.694 12057 Z= 0.288 Chirality : 0.039 0.142 1302 Planarity : 0.005 0.062 1565 Dihedral : 7.751 86.963 1250 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.54 % Allowed : 7.83 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.26), residues: 1070 helix: 0.96 (0.23), residues: 474 sheet: -2.33 (0.37), residues: 175 loop : -1.40 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.012 0.001 TYR B 238 PHE 0.010 0.001 PHE A 276 TRP 0.008 0.001 TRP A 49 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8889) covalent geometry : angle 0.55606 (12057) hydrogen bonds : bond 0.04489 ( 431) hydrogen bonds : angle 5.32182 ( 1238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 GLU cc_start: 0.7852 (tp30) cc_final: 0.7468 (tt0) REVERT: C 81 ASP cc_start: 0.8647 (t0) cc_final: 0.8350 (t0) REVERT: C 234 TYR cc_start: 0.8598 (m-10) cc_final: 0.8235 (m-10) REVERT: A 31 GLU cc_start: 0.7711 (tp30) cc_final: 0.7464 (tp30) REVERT: A 286 MET cc_start: 0.8143 (mmt) cc_final: 0.7003 (mmt) outliers start: 5 outliers final: 5 residues processed: 218 average time/residue: 0.2272 time to fit residues: 65.2768 Evaluate side-chains 204 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS D 109 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.129861 restraints weight = 37696.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.135361 restraints weight = 14591.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.138699 restraints weight = 7436.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.140805 restraints weight = 4665.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.142014 restraints weight = 3409.413| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8889 Z= 0.147 Angle : 0.535 4.856 12057 Z= 0.276 Chirality : 0.038 0.142 1302 Planarity : 0.004 0.051 1565 Dihedral : 7.205 78.684 1242 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.09 % Allowed : 10.00 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1070 helix: 1.26 (0.23), residues: 474 sheet: -2.29 (0.37), residues: 175 loop : -1.37 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.013 0.001 TYR A 238 PHE 0.008 0.001 PHE A 276 TRP 0.010 0.001 TRP B 142 HIS 0.003 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8889) covalent geometry : angle 0.53529 (12057) hydrogen bonds : bond 0.04063 ( 431) hydrogen bonds : angle 5.14267 ( 1238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 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: symmetry clash REVERT: C 32 GLU cc_start: 0.7805 (tp30) cc_final: 0.7562 (tt0) REVERT: C 81 ASP cc_start: 0.8737 (t0) cc_final: 0.8509 (t0) REVERT: C 196 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7510 (mmtm) REVERT: C 224 ASP cc_start: 0.7957 (t70) cc_final: 0.7701 (t70) REVERT: C 234 TYR cc_start: 0.8627 (m-10) cc_final: 0.8353 (m-10) REVERT: D 109 ASN cc_start: 0.7168 (m-40) cc_final: 0.6655 (m-40) REVERT: A 31 GLU cc_start: 0.7786 (tp30) cc_final: 0.7522 (tp30) REVERT: B 9 GLN cc_start: 0.7767 (tp40) cc_final: 0.7417 (tp-100) REVERT: B 101 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7723 (mmtt) outliers start: 10 outliers final: 6 residues processed: 209 average time/residue: 0.2207 time to fit residues: 60.8024 Evaluate side-chains 206 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 216 HIS D 216 HIS D 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.147444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.123740 restraints weight = 40969.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.129273 restraints weight = 15387.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.132730 restraints weight = 7727.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.134879 restraints weight = 4784.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.136031 restraints weight = 3448.327| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8889 Z= 0.216 Angle : 0.573 4.626 12057 Z= 0.300 Chirality : 0.040 0.137 1302 Planarity : 0.005 0.047 1565 Dihedral : 6.870 82.081 1236 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.96 % Allowed : 11.41 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1070 helix: 1.28 (0.23), residues: 475 sheet: -2.42 (0.37), residues: 177 loop : -1.41 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.013 0.002 TYR A 238 PHE 0.009 0.002 PHE D 223 TRP 0.011 0.001 TRP B 142 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8889) covalent geometry : angle 0.57278 (12057) hydrogen bonds : bond 0.04249 ( 431) hydrogen bonds : angle 5.21994 ( 1238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7990 (mtt-85) REVERT: C 72 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: C 81 ASP cc_start: 0.8755 (t0) cc_final: 0.8367 (t0) REVERT: C 224 ASP cc_start: 0.8059 (t70) cc_final: 0.7761 (t70) REVERT: C 234 TYR cc_start: 0.8688 (m-10) cc_final: 0.8339 (m-10) REVERT: A 31 GLU cc_start: 0.7681 (tp30) cc_final: 0.7457 (tp30) REVERT: A 286 MET cc_start: 0.8323 (mmt) cc_final: 0.7618 (mmt) REVERT: A 293 LEU cc_start: 0.8478 (mm) cc_final: 0.8148 (mm) REVERT: B 9 GLN cc_start: 0.7475 (tp40) cc_final: 0.7264 (tp-100) REVERT: B 101 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7728 (mmtt) outliers start: 18 outliers final: 14 residues processed: 216 average time/residue: 0.2377 time to fit residues: 66.4732 Evaluate side-chains 214 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 97 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 220 GLN D 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.151317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.128954 restraints weight = 34333.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.134171 restraints weight = 13522.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.137394 restraints weight = 6999.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.139484 restraints weight = 4422.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.140660 restraints weight = 3212.266| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8889 Z= 0.110 Angle : 0.507 4.471 12057 Z= 0.260 Chirality : 0.038 0.140 1302 Planarity : 0.004 0.047 1565 Dihedral : 6.553 87.674 1236 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 13.70 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1070 helix: 1.53 (0.24), residues: 481 sheet: -2.23 (0.38), residues: 175 loop : -1.38 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.011 0.001 TYR B 238 PHE 0.011 0.001 PHE A 276 TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8889) covalent geometry : angle 0.50693 (12057) hydrogen bonds : bond 0.03665 ( 431) hydrogen bonds : angle 4.95537 ( 1238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 36 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7865 (mtt-85) REVERT: C 72 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: C 81 ASP cc_start: 0.8666 (t0) cc_final: 0.8339 (t0) REVERT: C 224 ASP cc_start: 0.8064 (t70) cc_final: 0.7788 (t70) REVERT: C 234 TYR cc_start: 0.8612 (m-10) cc_final: 0.8276 (m-10) REVERT: D 86 ASN cc_start: 0.8291 (t0) cc_final: 0.8068 (t0) REVERT: A 31 GLU cc_start: 0.7727 (tp30) cc_final: 0.7446 (tp30) REVERT: A 286 MET cc_start: 0.8320 (mmt) cc_final: 0.7529 (mmt) REVERT: B 9 GLN cc_start: 0.7521 (tp40) cc_final: 0.7184 (tp-100) REVERT: B 101 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7703 (mmtt) REVERT: B 191 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7841 (mtt180) outliers start: 11 outliers final: 6 residues processed: 217 average time/residue: 0.2296 time to fit residues: 65.0149 Evaluate side-chains 212 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 109 ASN D 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.152175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.129129 restraints weight = 39157.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.134629 restraints weight = 14847.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.138088 restraints weight = 7496.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.140240 restraints weight = 4604.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.141649 restraints weight = 3286.546| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8889 Z= 0.105 Angle : 0.496 5.642 12057 Z= 0.254 Chirality : 0.037 0.138 1302 Planarity : 0.004 0.054 1565 Dihedral : 6.303 88.217 1236 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.20 % Allowed : 13.26 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1070 helix: 1.73 (0.24), residues: 487 sheet: -2.14 (0.37), residues: 177 loop : -1.29 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 246 TYR 0.010 0.001 TYR A 238 PHE 0.015 0.001 PHE A 276 TRP 0.010 0.001 TRP D 191 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8889) covalent geometry : angle 0.49631 (12057) hydrogen bonds : bond 0.03448 ( 431) hydrogen bonds : angle 4.77257 ( 1238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7998 (tp) REVERT: C 72 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: C 81 ASP cc_start: 0.8634 (t0) cc_final: 0.8298 (t0) REVERT: C 128 ASN cc_start: 0.8177 (p0) cc_final: 0.7749 (p0) REVERT: C 224 ASP cc_start: 0.8091 (t70) cc_final: 0.7803 (t70) REVERT: C 234 TYR cc_start: 0.8583 (m-10) cc_final: 0.8261 (m-10) REVERT: D 74 MET cc_start: 0.6515 (mpp) cc_final: 0.6138 (mtt) REVERT: D 109 ASN cc_start: 0.7030 (m-40) cc_final: 0.6501 (m-40) REVERT: A 31 GLU cc_start: 0.7731 (tp30) cc_final: 0.7453 (tp30) REVERT: A 286 MET cc_start: 0.8393 (mmt) cc_final: 0.7603 (mmt) REVERT: A 293 LEU cc_start: 0.8516 (mm) cc_final: 0.8197 (mm) REVERT: B 9 GLN cc_start: 0.7648 (tp40) cc_final: 0.7250 (tp-100) REVERT: B 101 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7690 (mmtt) REVERT: B 209 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7035 (tm130) REVERT: B 269 TRP cc_start: 0.8356 (m-10) cc_final: 0.7765 (m-10) outliers start: 11 outliers final: 5 residues processed: 214 average time/residue: 0.2644 time to fit residues: 74.6333 Evaluate side-chains 211 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.150529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.126817 restraints weight = 42927.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.132531 restraints weight = 15904.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.136082 restraints weight = 7891.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.138290 restraints weight = 4804.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.139781 restraints weight = 3410.588| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8889 Z= 0.149 Angle : 0.518 4.577 12057 Z= 0.265 Chirality : 0.038 0.140 1302 Planarity : 0.004 0.046 1565 Dihedral : 6.391 86.779 1236 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.85 % Allowed : 13.04 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.26), residues: 1070 helix: 1.73 (0.24), residues: 487 sheet: -2.16 (0.37), residues: 177 loop : -1.35 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.012 0.001 TYR B 167 PHE 0.014 0.001 PHE A 276 TRP 0.009 0.001 TRP D 191 HIS 0.006 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8889) covalent geometry : angle 0.51752 (12057) hydrogen bonds : bond 0.03606 ( 431) hydrogen bonds : angle 4.86647 ( 1238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8060 (tp) REVERT: C 36 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8061 (mtt-85) REVERT: C 72 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: C 96 TRP cc_start: 0.8790 (m-10) cc_final: 0.8280 (m-10) REVERT: C 224 ASP cc_start: 0.8250 (t70) cc_final: 0.7940 (t70) REVERT: C 234 TYR cc_start: 0.8602 (m-10) cc_final: 0.8285 (m-10) REVERT: D 9 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8181 (tm) REVERT: D 74 MET cc_start: 0.6810 (mpp) cc_final: 0.6505 (mtt) REVERT: A 31 GLU cc_start: 0.7761 (tp30) cc_final: 0.7484 (tp30) REVERT: A 286 MET cc_start: 0.8481 (mmt) cc_final: 0.7639 (mmt) REVERT: A 293 LEU cc_start: 0.8523 (mm) cc_final: 0.8176 (mm) REVERT: B 9 GLN cc_start: 0.7541 (tp40) cc_final: 0.7117 (tp-100) REVERT: B 46 GLU cc_start: 0.7650 (pm20) cc_final: 0.7340 (mm-30) REVERT: B 101 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7700 (mmtt) REVERT: B 269 TRP cc_start: 0.8334 (m-10) cc_final: 0.7742 (m-10) outliers start: 17 outliers final: 11 residues processed: 213 average time/residue: 0.2695 time to fit residues: 75.2340 Evaluate side-chains 216 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 211 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 109 ASN D 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.152329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.129338 restraints weight = 36734.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.134799 restraints weight = 14229.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.138157 restraints weight = 7275.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.140311 restraints weight = 4542.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.141727 restraints weight = 3265.113| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8889 Z= 0.113 Angle : 0.499 5.016 12057 Z= 0.254 Chirality : 0.038 0.154 1302 Planarity : 0.004 0.047 1565 Dihedral : 6.195 84.518 1236 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.63 % Allowed : 13.91 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 1070 helix: 1.80 (0.24), residues: 487 sheet: -2.09 (0.38), residues: 177 loop : -1.29 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.010 0.001 TYR A 238 PHE 0.018 0.001 PHE A 276 TRP 0.009 0.001 TRP D 114 HIS 0.006 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8889) covalent geometry : angle 0.49853 (12057) hydrogen bonds : bond 0.03422 ( 431) hydrogen bonds : angle 4.75540 ( 1238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 36 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8034 (mtt-85) REVERT: C 72 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: C 81 ASP cc_start: 0.8442 (t0) cc_final: 0.7993 (t0) REVERT: C 96 TRP cc_start: 0.8804 (m-10) cc_final: 0.8102 (m-10) REVERT: C 188 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7775 (tp) REVERT: C 224 ASP cc_start: 0.8275 (t70) cc_final: 0.7974 (t70) REVERT: C 234 TYR cc_start: 0.8584 (m-10) cc_final: 0.8291 (m-10) REVERT: D 74 MET cc_start: 0.6658 (mpp) cc_final: 0.6360 (mtt) REVERT: D 109 ASN cc_start: 0.7018 (m-40) cc_final: 0.6475 (m-40) REVERT: A 31 GLU cc_start: 0.7743 (tp30) cc_final: 0.7465 (tp30) REVERT: A 211 LEU cc_start: 0.8069 (mt) cc_final: 0.7783 (mt) REVERT: A 286 MET cc_start: 0.8437 (mmt) cc_final: 0.7770 (mmt) REVERT: A 293 LEU cc_start: 0.8526 (mm) cc_final: 0.8196 (mm) REVERT: B 9 GLN cc_start: 0.7511 (tp40) cc_final: 0.7033 (tp-100) REVERT: B 101 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7710 (mmtt) outliers start: 15 outliers final: 8 residues processed: 219 average time/residue: 0.2534 time to fit residues: 72.3155 Evaluate side-chains 215 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 211 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 220 GLN ** B 163 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.152382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.129558 restraints weight = 36325.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.134952 restraints weight = 14178.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.138371 restraints weight = 7252.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.140409 restraints weight = 4498.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.141831 restraints weight = 3247.550| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8889 Z= 0.107 Angle : 0.491 5.594 12057 Z= 0.249 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.046 1565 Dihedral : 6.046 81.940 1236 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.09 % Allowed : 15.11 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1070 helix: 1.92 (0.24), residues: 485 sheet: -2.03 (0.38), residues: 177 loop : -1.21 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.010 0.001 TYR B 238 PHE 0.016 0.001 PHE A 276 TRP 0.010 0.001 TRP D 191 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8889) covalent geometry : angle 0.49111 (12057) hydrogen bonds : bond 0.03289 ( 431) hydrogen bonds : angle 4.67632 ( 1238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8051 (tp) REVERT: C 36 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8039 (mtt-85) REVERT: C 72 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: C 81 ASP cc_start: 0.8386 (t0) cc_final: 0.7931 (t0) REVERT: C 96 TRP cc_start: 0.8769 (m-10) cc_final: 0.7807 (m-10) REVERT: C 188 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7738 (tp) REVERT: C 224 ASP cc_start: 0.8274 (t70) cc_final: 0.7985 (t70) REVERT: C 234 TYR cc_start: 0.8583 (m-10) cc_final: 0.8288 (m-10) REVERT: D 74 MET cc_start: 0.6782 (mpp) cc_final: 0.6426 (mtt) REVERT: D 80 VAL cc_start: 0.8867 (p) cc_final: 0.8520 (t) REVERT: A 31 GLU cc_start: 0.7772 (tp30) cc_final: 0.7490 (tp30) REVERT: A 286 MET cc_start: 0.8454 (mmt) cc_final: 0.7770 (mmt) REVERT: A 293 LEU cc_start: 0.8546 (mm) cc_final: 0.8187 (mm) REVERT: B 101 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7703 (mmtt) REVERT: B 269 TRP cc_start: 0.8265 (m-10) cc_final: 0.7672 (m-10) outliers start: 10 outliers final: 5 residues processed: 216 average time/residue: 0.2890 time to fit residues: 81.0381 Evaluate side-chains 217 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 109 ASN D 220 GLN B 9 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.151879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.128593 restraints weight = 38515.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.134181 restraints weight = 14688.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.137687 restraints weight = 7377.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.139656 restraints weight = 4530.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.141184 restraints weight = 3315.529| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8889 Z= 0.126 Angle : 0.502 5.255 12057 Z= 0.255 Chirality : 0.038 0.137 1302 Planarity : 0.004 0.043 1565 Dihedral : 6.035 81.308 1236 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.20 % Allowed : 14.89 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1070 helix: 1.93 (0.24), residues: 485 sheet: -2.04 (0.38), residues: 177 loop : -1.24 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.010 0.001 TYR A 238 PHE 0.020 0.001 PHE A 276 TRP 0.010 0.001 TRP B 49 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8889) covalent geometry : angle 0.50218 (12057) hydrogen bonds : bond 0.03412 ( 431) hydrogen bonds : angle 4.71999 ( 1238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8058 (tp) REVERT: C 36 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8068 (mtt-85) REVERT: C 72 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: C 81 ASP cc_start: 0.8391 (t0) cc_final: 0.7893 (t0) REVERT: C 188 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7738 (tp) REVERT: C 224 ASP cc_start: 0.8314 (t70) cc_final: 0.8005 (t70) REVERT: C 234 TYR cc_start: 0.8599 (m-10) cc_final: 0.8300 (m-10) REVERT: D 80 VAL cc_start: 0.8876 (p) cc_final: 0.8539 (t) REVERT: D 109 ASN cc_start: 0.7097 (m-40) cc_final: 0.6570 (m-40) REVERT: A 31 GLU cc_start: 0.7751 (tp30) cc_final: 0.7466 (tp30) REVERT: A 211 LEU cc_start: 0.8054 (mt) cc_final: 0.7827 (mt) REVERT: A 286 MET cc_start: 0.8445 (mmt) cc_final: 0.7750 (mmt) REVERT: A 293 LEU cc_start: 0.8572 (mm) cc_final: 0.8221 (mm) REVERT: B 101 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7700 (mmtt) REVERT: B 210 ARG cc_start: 0.7409 (ppt170) cc_final: 0.6729 (mtm-85) REVERT: B 269 TRP cc_start: 0.8316 (m-10) cc_final: 0.7674 (m-10) outliers start: 11 outliers final: 7 residues processed: 213 average time/residue: 0.2920 time to fit residues: 80.1530 Evaluate side-chains 217 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 220 GLN ** B 163 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.153426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.129658 restraints weight = 43698.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.135465 restraints weight = 16161.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.139107 restraints weight = 7978.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.141291 restraints weight = 4825.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.142821 restraints weight = 3410.176| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8889 Z= 0.100 Angle : 0.490 4.988 12057 Z= 0.248 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.044 1565 Dihedral : 5.875 78.836 1236 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.09 % Allowed : 15.11 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1070 helix: 1.98 (0.24), residues: 486 sheet: -1.83 (0.40), residues: 157 loop : -1.16 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.009 0.001 TYR B 238 PHE 0.018 0.001 PHE A 276 TRP 0.012 0.001 TRP B 49 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8889) covalent geometry : angle 0.49004 (12057) hydrogen bonds : bond 0.03241 ( 431) hydrogen bonds : angle 4.63082 ( 1238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.49 seconds wall clock time: 56 minutes 15.30 seconds (3375.30 seconds total)