Starting phenix.real_space_refine on Wed May 21 03:02:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dq0_27645/05_2025/8dq0_27645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dq0_27645/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dq0_27645/05_2025/8dq0_27645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dq0_27645/05_2025/8dq0_27645.map" model { file = "/net/cci-nas-00/data/ceres_data/8dq0_27645/05_2025/8dq0_27645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dq0_27645/05_2025/8dq0_27645_trim.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.082 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.29, per 1000 atoms: 0.66 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: 4.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.26 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: 5.56 Time building geometry restraints manager: 5.43 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 241 or resid 3 \ 01)) 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 241 or resid 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.270 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (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 TRP 0.012 0.001 TRP B 269 HIS 0.011 0.001 HIS B 69 PHE 0.014 0.002 PHE D 101 TYR 0.032 0.003 TYR C 72 ARG 0.025 0.001 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.16524 ( 431) hydrogen bonds : angle 6.65636 ( 1238) covalent geometry : bond 0.00844 ( 8889) covalent geometry : angle 0.98109 (12057) *********************** 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 : 1.296 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: 0.5468 time to fit residues: 163.0662 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 : 1.189 ------------------------------------------------------------------------------- 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 88 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** 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 = 0.3496 r_free = 0.3496 target = 0.150578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.126966 restraints weight = 37153.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.132321 restraints weight = 14548.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.135618 restraints weight = 7519.833| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8889 Z= 0.212 Angle : 0.596 5.034 12057 Z= 0.312 Chirality : 0.040 0.142 1302 Planarity : 0.005 0.063 1565 Dihedral : 7.707 77.895 1250 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.87 % Allowed : 8.04 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1070 helix: 0.86 (0.23), residues: 475 sheet: -2.58 (0.36), residues: 175 loop : -1.42 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 49 HIS 0.005 0.001 HIS A 74 PHE 0.010 0.001 PHE A 276 TYR 0.012 0.001 TYR C 77 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 431) hydrogen bonds : angle 5.42175 ( 1238) covalent geometry : bond 0.00484 ( 8889) covalent geometry : angle 0.59577 (12057) *********************** 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 226 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 1.399 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: 0.7892 (tp30) cc_final: 0.7577 (tt0) REVERT: C 81 ASP cc_start: 0.8814 (t0) cc_final: 0.8581 (t0) REVERT: C 224 ASP cc_start: 0.7984 (t70) cc_final: 0.7743 (t70) REVERT: C 234 TYR cc_start: 0.8652 (m-10) cc_final: 0.8374 (m-10) REVERT: A 31 GLU cc_start: 0.7683 (tp30) cc_final: 0.7468 (tp30) outliers start: 8 outliers final: 7 residues processed: 222 average time/residue: 0.5129 time to fit residues: 150.6192 Evaluate side-chains 209 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 229 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain A residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN A 98 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.151592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.127760 restraints weight = 42680.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.133416 restraints weight = 15787.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.136945 restraints weight = 7869.411| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1894 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= 0.130 Angle : 0.525 5.090 12057 Z= 0.271 Chirality : 0.038 0.139 1302 Planarity : 0.004 0.051 1565 Dihedral : 7.195 78.880 1242 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.20 % Allowed : 10.22 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1070 helix: 1.18 (0.23), residues: 474 sheet: -2.37 (0.37), residues: 173 loop : -1.39 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 142 HIS 0.003 0.001 HIS B 149 PHE 0.008 0.001 PHE A 276 TYR 0.011 0.001 TYR B 238 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 431) hydrogen bonds : angle 5.11652 ( 1238) covalent geometry : bond 0.00292 ( 8889) covalent geometry : angle 0.52512 (12057) *********************** 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 215 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 1.192 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: 0.7835 (tp30) cc_final: 0.7592 (tt0) REVERT: C 74 MET cc_start: 0.6734 (mtt) cc_final: 0.6499 (mtt) REVERT: C 81 ASP cc_start: 0.8754 (t0) cc_final: 0.8552 (t0) REVERT: C 234 TYR cc_start: 0.8625 (m-10) cc_final: 0.8278 (m-10) REVERT: A 31 GLU cc_start: 0.7739 (tp30) cc_final: 0.7471 (tp30) REVERT: B 101 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7763 (mmtt) outliers start: 11 outliers final: 8 residues processed: 208 average time/residue: 0.5365 time to fit residues: 146.2789 Evaluate side-chains 204 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 205 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN D 109 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3497 r_free = 0.3497 target = 0.151073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.127750 restraints weight = 39216.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.133266 restraints weight = 14956.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.136566 restraints weight = 7580.217| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 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 = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8889 Z= 0.133 Angle : 0.509 4.588 12057 Z= 0.262 Chirality : 0.038 0.142 1302 Planarity : 0.004 0.046 1565 Dihedral : 6.677 82.607 1236 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.52 % Allowed : 11.74 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1070 helix: 1.42 (0.23), residues: 487 sheet: -2.35 (0.37), residues: 177 loop : -1.40 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 142 HIS 0.003 0.001 HIS C 171 PHE 0.017 0.001 PHE A 276 TYR 0.011 0.001 TYR A 238 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 431) hydrogen bonds : angle 5.00059 ( 1238) covalent geometry : bond 0.00305 ( 8889) covalent geometry : angle 0.50861 (12057) *********************** 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 221 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: C 81 ASP cc_start: 0.8738 (t0) cc_final: 0.8397 (t0) REVERT: C 196 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7449 (mmtm) REVERT: C 234 TYR cc_start: 0.8629 (m-10) cc_final: 0.8291 (m-10) REVERT: D 9 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7976 (tm) REVERT: D 109 ASN cc_start: 0.7055 (m-40) cc_final: 0.6517 (m-40) REVERT: A 31 GLU cc_start: 0.7767 (tp30) cc_final: 0.7497 (tp30) REVERT: A 286 MET cc_start: 0.8325 (mmt) cc_final: 0.7575 (mmt) REVERT: B 101 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7695 (mmtt) REVERT: B 269 TRP cc_start: 0.8237 (m-10) cc_final: 0.7587 (m-10) outliers start: 14 outliers final: 9 residues processed: 211 average time/residue: 0.5117 time to fit residues: 142.0259 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 : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 72 TYR 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 162 LEU 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 B residue 53 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 220 GLN D 216 HIS D 220 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 = 0.3501 r_free = 0.3501 target = 0.151236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.128057 restraints weight = 39033.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.133487 restraints weight = 14841.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.136966 restraints weight = 7518.687| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8889 Z= 0.124 Angle : 0.499 4.565 12057 Z= 0.257 Chirality : 0.038 0.138 1302 Planarity : 0.004 0.044 1565 Dihedral : 6.522 85.736 1236 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.41 % Allowed : 12.28 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1070 helix: 1.60 (0.24), residues: 487 sheet: -2.26 (0.37), residues: 177 loop : -1.36 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 191 HIS 0.003 0.001 HIS B 149 PHE 0.009 0.001 PHE A 276 TYR 0.011 0.001 TYR A 238 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 431) hydrogen bonds : angle 4.87267 ( 1238) covalent geometry : bond 0.00282 ( 8889) covalent geometry : angle 0.49949 (12057) *********************** 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 222 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8174 (tp) REVERT: C 36 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7986 (mtt-85) REVERT: C 72 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: C 81 ASP cc_start: 0.8664 (t0) cc_final: 0.8308 (t0) REVERT: C 224 ASP cc_start: 0.8115 (t70) cc_final: 0.7830 (t70) REVERT: C 234 TYR cc_start: 0.8639 (m-10) cc_final: 0.8295 (m-10) REVERT: D 9 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7997 (tm) REVERT: D 220 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7011 (mm110) REVERT: A 31 GLU cc_start: 0.7741 (tp30) cc_final: 0.7466 (tp30) REVERT: A 286 MET cc_start: 0.8406 (mmt) cc_final: 0.7658 (mmt) REVERT: A 293 LEU cc_start: 0.8507 (mm) cc_final: 0.8159 (mm) REVERT: B 46 GLU cc_start: 0.7858 (pm20) cc_final: 0.7361 (mm-30) REVERT: B 101 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7697 (mmtt) REVERT: B 269 TRP cc_start: 0.8276 (m-10) cc_final: 0.7773 (m-10) outliers start: 13 outliers final: 6 residues processed: 216 average time/residue: 0.5221 time to fit residues: 150.2554 Evaluate side-chains 214 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 D residue 220 GLN Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 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 B 9 GLN ** B 163 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.151792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.128672 restraints weight = 39072.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.134179 restraints weight = 14745.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.137658 restraints weight = 7428.009| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2369 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 : 0.492 4.536 12057 Z= 0.252 Chirality : 0.038 0.138 1302 Planarity : 0.004 0.041 1565 Dihedral : 6.425 87.881 1236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.09 % Allowed : 13.59 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1070 helix: 1.68 (0.24), residues: 487 sheet: -2.21 (0.37), residues: 177 loop : -1.34 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS B 149 PHE 0.015 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 431) hydrogen bonds : angle 4.78830 ( 1238) covalent geometry : bond 0.00259 ( 8889) covalent geometry : angle 0.49192 (12057) *********************** 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 217 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8168 (tp) REVERT: C 72 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: C 81 ASP cc_start: 0.8638 (t0) cc_final: 0.8332 (t0) REVERT: C 224 ASP cc_start: 0.8152 (t70) cc_final: 0.7854 (t70) REVERT: C 234 TYR cc_start: 0.8637 (m-10) cc_final: 0.8294 (m-10) REVERT: D 9 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8055 (tm) REVERT: D 74 MET cc_start: 0.6526 (mpp) cc_final: 0.6172 (mtt) REVERT: D 109 ASN cc_start: 0.6979 (m-40) cc_final: 0.6408 (m-40) REVERT: A 31 GLU cc_start: 0.7744 (tp30) cc_final: 0.7471 (tp30) REVERT: A 286 MET cc_start: 0.8488 (mmt) cc_final: 0.7623 (mmt) REVERT: A 293 LEU cc_start: 0.8523 (mm) cc_final: 0.8150 (mm) REVERT: B 46 GLU cc_start: 0.7860 (pm20) cc_final: 0.7341 (mm-30) REVERT: B 101 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7690 (mmtt) REVERT: B 269 TRP cc_start: 0.8270 (m-10) cc_final: 0.7699 (m-10) outliers start: 10 outliers final: 6 residues processed: 213 average time/residue: 0.5206 time to fit residues: 146.3266 Evaluate side-chains 210 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 A residue 160 SER Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 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 = 0.150336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.127458 restraints weight = 37326.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.132857 restraints weight = 14338.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.136208 restraints weight = 7314.146| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 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 = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8889 Z= 0.142 Angle : 0.506 4.576 12057 Z= 0.260 Chirality : 0.038 0.137 1302 Planarity : 0.004 0.041 1565 Dihedral : 6.452 89.208 1236 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.52 % Allowed : 13.48 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1070 helix: 1.72 (0.24), residues: 487 sheet: -2.22 (0.37), residues: 177 loop : -1.37 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 191 HIS 0.003 0.001 HIS B 149 PHE 0.015 0.001 PHE A 276 TYR 0.011 0.001 TYR A 238 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 431) hydrogen bonds : angle 4.80377 ( 1238) covalent geometry : bond 0.00327 ( 8889) covalent geometry : angle 0.50587 (12057) *********************** 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 223 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 36 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8042 (mtt-85) REVERT: C 72 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: C 81 ASP cc_start: 0.8669 (t0) cc_final: 0.8357 (t0) REVERT: C 224 ASP cc_start: 0.8317 (t70) cc_final: 0.7999 (t70) REVERT: C 234 TYR cc_start: 0.8673 (m-10) cc_final: 0.8358 (m-10) REVERT: D 9 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8013 (tm) REVERT: D 74 MET cc_start: 0.6891 (mpp) cc_final: 0.6579 (mtt) REVERT: A 31 GLU cc_start: 0.7778 (tp30) cc_final: 0.7499 (tp30) REVERT: A 286 MET cc_start: 0.8488 (mmt) cc_final: 0.7689 (mmt) REVERT: A 293 LEU cc_start: 0.8520 (mm) cc_final: 0.8125 (mm) REVERT: B 46 GLU cc_start: 0.7599 (pm20) cc_final: 0.7297 (mm-30) REVERT: B 101 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7696 (mmtt) outliers start: 14 outliers final: 8 residues processed: 215 average time/residue: 0.5548 time to fit residues: 155.4762 Evaluate side-chains 213 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 B residue 53 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 9 GLN ** B 163 HIS ** 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 = 0.3498 r_free = 0.3498 target = 0.151048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.128279 restraints weight = 36334.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.133548 restraints weight = 14004.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.136937 restraints weight = 7209.578| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2576 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= 0.120 Angle : 0.495 4.553 12057 Z= 0.253 Chirality : 0.037 0.138 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.294 86.571 1236 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.09 % Allowed : 14.24 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1070 helix: 1.78 (0.24), residues: 487 sheet: -2.17 (0.38), residues: 171 loop : -1.25 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS B 149 PHE 0.014 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 431) hydrogen bonds : angle 4.74061 ( 1238) covalent geometry : bond 0.00278 ( 8889) covalent geometry : angle 0.49495 (12057) *********************** 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 220 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8143 (tp) REVERT: C 36 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8063 (mtt-85) REVERT: C 72 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: C 96 TRP cc_start: 0.8776 (m-10) cc_final: 0.8199 (m-10) REVERT: C 224 ASP cc_start: 0.8334 (t70) cc_final: 0.8019 (t70) REVERT: C 234 TYR cc_start: 0.8677 (m-10) cc_final: 0.8361 (m-10) REVERT: D 9 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (tm) REVERT: D 74 MET cc_start: 0.6828 (mpp) cc_final: 0.6583 (mtt) REVERT: D 109 ASN cc_start: 0.7001 (m-40) cc_final: 0.6421 (m-40) REVERT: A 31 GLU cc_start: 0.7761 (tp30) cc_final: 0.7479 (tp30) REVERT: A 286 MET cc_start: 0.8465 (mmt) cc_final: 0.7778 (mmt) REVERT: A 293 LEU cc_start: 0.8527 (mm) cc_final: 0.8156 (mm) REVERT: B 101 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7704 (mmtt) outliers start: 10 outliers final: 7 residues processed: 216 average time/residue: 0.5474 time to fit residues: 154.8208 Evaluate side-chains 215 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.151513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.128161 restraints weight = 39241.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.133732 restraints weight = 14785.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.137231 restraints weight = 7410.574| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2631 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= 0.115 Angle : 0.493 4.908 12057 Z= 0.251 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.169 84.593 1236 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.52 % Allowed : 14.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1070 helix: 1.87 (0.24), residues: 485 sheet: -2.11 (0.39), residues: 171 loop : -1.20 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS B 149 PHE 0.018 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 431) hydrogen bonds : angle 4.69934 ( 1238) covalent geometry : bond 0.00265 ( 8889) covalent geometry : angle 0.49320 (12057) *********************** 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 218 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8141 (tp) REVERT: C 36 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8068 (mtt-85) REVERT: C 72 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: C 81 ASP cc_start: 0.8456 (t0) cc_final: 0.8031 (t0) REVERT: C 96 TRP cc_start: 0.8842 (m-10) cc_final: 0.8107 (m-10) REVERT: C 224 ASP cc_start: 0.8343 (t70) cc_final: 0.8043 (t70) REVERT: C 234 TYR cc_start: 0.8676 (m-10) cc_final: 0.8372 (m-10) REVERT: D 9 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (tm) REVERT: D 74 MET cc_start: 0.6850 (mpp) cc_final: 0.6583 (mtt) REVERT: D 80 VAL cc_start: 0.8877 (p) cc_final: 0.8552 (t) REVERT: A 31 GLU cc_start: 0.7767 (tp30) cc_final: 0.7489 (tp30) REVERT: A 286 MET cc_start: 0.8469 (mmt) cc_final: 0.7755 (mmt) REVERT: A 289 MET cc_start: 0.8227 (ttt) cc_final: 0.7340 (ttt) REVERT: A 293 LEU cc_start: 0.8550 (mm) cc_final: 0.8168 (mm) REVERT: B 101 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7703 (mmtt) outliers start: 14 outliers final: 8 residues processed: 212 average time/residue: 0.5476 time to fit residues: 150.5695 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 : 1.204 ------------------------------------------------------------------------------- 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 B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.151023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.128037 restraints weight = 37722.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.133483 restraints weight = 14414.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.136915 restraints weight = 7297.070| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2693 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= 0.123 Angle : 0.496 4.520 12057 Z= 0.253 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.139 83.488 1236 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.41 % Allowed : 14.57 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1070 helix: 1.88 (0.24), residues: 485 sheet: -2.08 (0.39), residues: 171 loop : -1.20 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS B 149 PHE 0.016 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 431) hydrogen bonds : angle 4.69595 ( 1238) covalent geometry : bond 0.00286 ( 8889) covalent geometry : angle 0.49566 (12057) ********************** 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 221 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 1.288 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: 0.8462 (OUTLIER) cc_final: 0.8146 (tp) REVERT: C 36 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8097 (mtt-85) REVERT: C 72 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: C 81 ASP cc_start: 0.8429 (t0) cc_final: 0.7922 (t0) REVERT: C 96 TRP cc_start: 0.8775 (m-10) cc_final: 0.8509 (m-10) REVERT: C 188 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (tp) REVERT: C 224 ASP cc_start: 0.8354 (t70) cc_final: 0.8036 (t70) REVERT: C 234 TYR cc_start: 0.8678 (m-10) cc_final: 0.8372 (m-10) REVERT: D 9 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8174 (tm) REVERT: D 74 MET cc_start: 0.6909 (mpp) cc_final: 0.6693 (mtt) REVERT: D 80 VAL cc_start: 0.8890 (p) cc_final: 0.8553 (t) REVERT: D 109 ASN cc_start: 0.7064 (m-40) cc_final: 0.6489 (m-40) REVERT: A 31 GLU cc_start: 0.7746 (tp30) cc_final: 0.7463 (tp30) REVERT: A 286 MET cc_start: 0.8472 (mmt) cc_final: 0.7768 (mmt) REVERT: A 289 MET cc_start: 0.8220 (ttt) cc_final: 0.7391 (ttt) REVERT: A 293 LEU cc_start: 0.8575 (mm) cc_final: 0.8184 (mm) REVERT: B 101 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7702 (mmtt) outliers start: 13 outliers final: 8 residues processed: 215 average time/residue: 0.5624 time to fit residues: 157.2525 Evaluate side-chains 219 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 220 GLN D 220 GLN B 9 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3512 r_free = 0.3512 target = 0.152314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.129327 restraints weight = 38330.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.134824 restraints weight = 14508.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.138225 restraints weight = 7308.697| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2714 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= 0.101 Angle : 0.488 4.871 12057 Z= 0.247 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.039 1565 Dihedral : 5.965 81.359 1236 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.52 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 1070 helix: 1.96 (0.24), residues: 485 sheet: -2.04 (0.38), residues: 177 loop : -1.18 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS B 149 PHE 0.015 0.001 PHE A 276 TYR 0.009 0.001 TYR A 238 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 431) hydrogen bonds : angle 4.61919 ( 1238) covalent geometry : bond 0.00233 ( 8889) covalent geometry : angle 0.48811 (12057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.06 seconds wall clock time: 105 minutes 31.02 seconds (6331.02 seconds total)