Starting phenix.real_space_refine on Wed Jun 18 06:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dq0_27645/06_2025/8dq0_27645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dq0_27645/06_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_27645/06_2025/8dq0_27645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dq0_27645/06_2025/8dq0_27645.map" model { file = "/net/cci-nas-00/data/ceres_data/8dq0_27645/06_2025/8dq0_27645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dq0_27645/06_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-5710/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: 11.66, per 1000 atoms: 0.68 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: 4.39 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: 1.37 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: 5.85 Time building geometry restraints manager: 5.19 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: 0.290 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.540 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.680 ------------------------------------------------------------------------------- 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 : 1.240 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: 0.5525 time to fit residues: 165.2136 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 : 1.246 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.126969 restraints weight = 37153.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.132321 restraints weight = 14532.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.135655 restraints weight = 7526.903| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.136 | | 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) = 0.136 | | 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 : 1.217 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: 0.7897 (tp30) cc_final: 0.7579 (tt0) REVERT: C 81 ASP cc_start: 0.8815 (t0) cc_final: 0.8582 (t0) REVERT: C 224 ASP cc_start: 0.7978 (t70) cc_final: 0.7736 (t70) REVERT: C 234 TYR cc_start: 0.8653 (m-10) cc_final: 0.8373 (m-10) REVERT: A 31 GLU cc_start: 0.7679 (tp30) cc_final: 0.7463 (tp30) outliers start: 8 outliers final: 7 residues processed: 222 average time/residue: 0.5174 time to fit residues: 152.4059 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 : 1.189 ------------------------------------------------------------------------------- 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 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: 0.0980 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: 0.8980 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.151866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.127962 restraints weight = 42613.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.133652 restraints weight = 15819.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.137129 restraints weight = 7897.639| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- 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: 17 | |-----------------------------------------------------------------------------| |-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: 0.7314 moved from start: 0.1915 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= 0.128 Angle : 0.523 5.158 12057 Z= 0.270 Chirality : 0.038 0.143 1302 Planarity : 0.004 0.051 1565 Dihedral : 7.154 79.641 1242 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.09 % Allowed : 10.22 % Favored : 88.70 % 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: -0.63 (0.26), residues: 1070 helix: 1.21 (0.23), residues: 474 sheet: -2.36 (0.37), residues: 173 loop : -1.37 (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 0.04002 ( 431) hydrogen bonds : angle 5.08276 ( 1238) covalent geometry : bond 0.00288 ( 8889) covalent geometry : angle 0.52324 (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 216 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 1.319 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: 0.7815 (tp30) cc_final: 0.7540 (tt0) REVERT: C 81 ASP cc_start: 0.8768 (t0) cc_final: 0.8559 (t0) REVERT: C 234 TYR cc_start: 0.8622 (m-10) cc_final: 0.8272 (m-10) REVERT: A 31 GLU cc_start: 0.7761 (tp30) cc_final: 0.7488 (tp30) REVERT: B 101 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7724 (mmtt) outliers start: 10 outliers final: 7 residues processed: 209 average time/residue: 0.5442 time to fit residues: 149.1942 Evaluate side-chains 204 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.150279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.126935 restraints weight = 39165.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.132386 restraints weight = 14973.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.135762 restraints weight = 7646.398| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 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 = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8889 Z= 0.155 Angle : 0.521 4.616 12057 Z= 0.269 Chirality : 0.038 0.137 1302 Planarity : 0.004 0.046 1565 Dihedral : 6.715 83.453 1236 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.63 % Allowed : 11.85 % Favored : 86.52 % 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: -0.47 (0.26), residues: 1070 helix: 1.41 (0.23), residues: 487 sheet: -2.39 (0.37), residues: 177 loop : -1.42 (0.29), 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 0.010 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 0.03898 ( 431) hydrogen bonds : angle 5.03972 ( 1238) covalent geometry : bond 0.00355 ( 8889) covalent geometry : angle 0.52129 (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 219 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: C 81 ASP cc_start: 0.8741 (t0) cc_final: 0.8415 (t0) REVERT: C 196 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7446 (mmtm) REVERT: C 224 ASP cc_start: 0.8097 (t70) cc_final: 0.7813 (t70) REVERT: C 234 TYR cc_start: 0.8655 (m-10) cc_final: 0.8302 (m-10) REVERT: D 9 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7985 (tm) REVERT: D 109 ASN cc_start: 0.7024 (m-40) cc_final: 0.6490 (m-40) REVERT: A 31 GLU cc_start: 0.7773 (tp30) cc_final: 0.7508 (tp30) REVERT: A 286 MET cc_start: 0.8336 (mmt) cc_final: 0.7580 (mmt) REVERT: B 101 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7707 (mmtt) REVERT: B 269 TRP cc_start: 0.8181 (m-10) cc_final: 0.7580 (m-10) outliers start: 15 outliers final: 11 residues processed: 210 average time/residue: 0.5392 time to fit residues: 151.6170 Evaluate side-chains 214 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 162 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain 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: 0.0770 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.151894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.128877 restraints weight = 38789.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.134359 restraints weight = 14731.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.137779 restraints weight = 7431.196| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 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 = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8889 Z= 0.108 Angle : 0.494 4.542 12057 Z= 0.253 Chirality : 0.037 0.138 1302 Planarity : 0.004 0.043 1565 Dihedral : 6.467 87.493 1236 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.41 % Allowed : 12.50 % Favored : 86.09 % 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: -0.26 (0.26), residues: 1070 helix: 1.63 (0.24), residues: 487 sheet: -2.26 (0.37), residues: 177 loop : -1.38 (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 C 171 PHE 0.013 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 431) hydrogen bonds : angle 4.82836 ( 1238) covalent geometry : bond 0.00246 ( 8889) covalent geometry : angle 0.49406 (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 225 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8178 (tp) REVERT: C 72 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: C 81 ASP cc_start: 0.8640 (t0) cc_final: 0.8316 (t0) REVERT: C 224 ASP cc_start: 0.8137 (t70) cc_final: 0.7856 (t70) REVERT: C 234 TYR cc_start: 0.8637 (m-10) cc_final: 0.8286 (m-10) REVERT: D 9 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8117 (tm) REVERT: D 220 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7064 (mm110) REVERT: A 31 GLU cc_start: 0.7734 (tp30) cc_final: 0.7459 (tp30) REVERT: A 286 MET cc_start: 0.8408 (mmt) cc_final: 0.7557 (mmt) REVERT: A 289 MET cc_start: 0.8307 (ttt) cc_final: 0.7399 (ttt) REVERT: A 293 LEU cc_start: 0.8496 (mm) cc_final: 0.8153 (mm) REVERT: B 46 GLU cc_start: 0.7854 (pm20) cc_final: 0.7362 (mm-30) REVERT: B 101 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7690 (mmtt) REVERT: B 269 TRP cc_start: 0.8262 (m-10) cc_final: 0.7758 (m-10) outliers start: 13 outliers final: 7 residues processed: 218 average time/residue: 0.5253 time to fit residues: 152.0953 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 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 56 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 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 D 220 GLN B 9 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.152039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.128919 restraints weight = 39006.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.134490 restraints weight = 14751.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.137884 restraints weight = 7421.271| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 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 = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2398 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= 0.114 Angle : 0.492 4.538 12057 Z= 0.252 Chirality : 0.037 0.135 1302 Planarity : 0.004 0.040 1565 Dihedral : 6.381 89.190 1236 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.20 % Allowed : 13.48 % 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: -0.16 (0.26), residues: 1070 helix: 1.69 (0.24), residues: 487 sheet: -2.17 (0.37), residues: 177 loop : -1.33 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 191 HIS 0.002 0.001 HIS B 149 PHE 0.016 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 0.03458 ( 431) hydrogen bonds : angle 4.76348 ( 1238) covalent geometry : bond 0.00261 ( 8889) covalent geometry : angle 0.49231 (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 214 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (tp) REVERT: C 72 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: C 81 ASP cc_start: 0.8640 (t0) cc_final: 0.8316 (t0) REVERT: C 196 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7441 (mmtm) REVERT: C 224 ASP cc_start: 0.8164 (t70) cc_final: 0.7863 (t70) REVERT: C 234 TYR cc_start: 0.8637 (m-10) cc_final: 0.8295 (m-10) REVERT: D 9 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8120 (tm) REVERT: D 74 MET cc_start: 0.6545 (mpp) cc_final: 0.6195 (mtt) REVERT: D 109 ASN cc_start: 0.6982 (m-40) cc_final: 0.6409 (m-40) REVERT: A 31 GLU cc_start: 0.7748 (tp30) cc_final: 0.7475 (tp30) REVERT: A 286 MET cc_start: 0.8433 (mmt) cc_final: 0.7629 (mmt) REVERT: B 46 GLU cc_start: 0.7855 (pm20) cc_final: 0.7342 (mm-30) REVERT: B 101 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7691 (mmtt) REVERT: B 269 TRP cc_start: 0.8255 (m-10) cc_final: 0.7702 (m-10) outliers start: 11 outliers final: 5 residues processed: 208 average time/residue: 0.5476 time to fit residues: 151.1938 Evaluate side-chains 208 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3518 r_free = 0.3518 target = 0.152783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.129803 restraints weight = 37713.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.135328 restraints weight = 14391.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.138715 restraints weight = 7267.192| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 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 = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8889 Z= 0.102 Angle : 0.483 4.497 12057 Z= 0.245 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.040 1565 Dihedral : 6.237 87.639 1236 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 13.80 % 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: -0.01 (0.26), residues: 1070 helix: 1.84 (0.24), residues: 487 sheet: -2.08 (0.38), residues: 177 loop : -1.29 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.002 0.000 HIS B 149 PHE 0.015 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 0.03301 ( 431) hydrogen bonds : angle 4.66314 ( 1238) covalent geometry : bond 0.00235 ( 8889) covalent geometry : angle 0.48258 (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 219 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8169 (tp) REVERT: C 72 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: C 81 ASP cc_start: 0.8628 (t0) cc_final: 0.8377 (t0) REVERT: C 96 TRP cc_start: 0.8837 (m-10) cc_final: 0.8225 (m-10) REVERT: C 224 ASP cc_start: 0.8277 (t70) cc_final: 0.7962 (t70) REVERT: C 234 TYR cc_start: 0.8629 (m-10) cc_final: 0.8301 (m-10) REVERT: D 9 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (tm) REVERT: D 74 MET cc_start: 0.6614 (mpp) cc_final: 0.6275 (mtt) REVERT: A 31 GLU cc_start: 0.7771 (tp30) cc_final: 0.7472 (tp30) REVERT: A 286 MET cc_start: 0.8384 (mmt) cc_final: 0.7696 (mmt) REVERT: B 46 GLU cc_start: 0.7613 (pm20) cc_final: 0.7184 (mm-30) REVERT: B 101 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7673 (mmtt) outliers start: 11 outliers final: 7 residues processed: 214 average time/residue: 0.5291 time to fit residues: 150.0398 Evaluate side-chains 210 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 117 CYS 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 A residue 277 LEU 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: 2.9990 chunk 10 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.151781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.128977 restraints weight = 36242.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.134316 restraints weight = 14039.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.137700 restraints weight = 7177.600| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 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 = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8889 Z= 0.117 Angle : 0.488 4.498 12057 Z= 0.249 Chirality : 0.037 0.137 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.207 85.625 1236 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.63 % Allowed : 13.80 % Favored : 84.57 % 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: 1.92 (0.24), residues: 485 sheet: -2.05 (0.38), residues: 177 loop : -1.25 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 114 HIS 0.002 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 0.03336 ( 431) hydrogen bonds : angle 4.67399 ( 1238) covalent geometry : bond 0.00274 ( 8889) covalent geometry : angle 0.48801 (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: 15 poor density : 205 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 36 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8044 (mtt-85) REVERT: C 72 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: C 96 TRP cc_start: 0.8804 (m-10) cc_final: 0.8124 (m-10) REVERT: C 224 ASP cc_start: 0.8304 (t70) cc_final: 0.7992 (t70) REVERT: C 234 TYR cc_start: 0.8630 (m-10) cc_final: 0.8332 (m-10) REVERT: D 9 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8255 (tm) REVERT: D 74 MET cc_start: 0.6785 (mpp) cc_final: 0.6488 (mtt) REVERT: D 109 ASN cc_start: 0.7072 (m-40) cc_final: 0.6504 (m-40) REVERT: A 31 GLU cc_start: 0.7741 (tp30) cc_final: 0.7472 (tp30) REVERT: A 211 LEU cc_start: 0.7957 (mt) cc_final: 0.7696 (mt) REVERT: A 286 MET cc_start: 0.8467 (mmt) cc_final: 0.7797 (mmt) REVERT: A 293 LEU cc_start: 0.8519 (mm) cc_final: 0.8118 (mm) REVERT: B 101 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7696 (mmtt) outliers start: 15 outliers final: 8 residues processed: 213 average time/residue: 0.5580 time to fit residues: 154.9377 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 : 1.246 ------------------------------------------------------------------------------- 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 117 CYS 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 Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 87 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.152529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.129326 restraints weight = 39319.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.134871 restraints weight = 14893.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.138335 restraints weight = 7516.410| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 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 = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.002 0.030 8889 Z= 0.104 Angle : 0.490 5.264 12057 Z= 0.250 Chirality : 0.037 0.139 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.123 84.469 1236 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: 0.15 (0.26), residues: 1070 helix: 1.99 (0.24), residues: 485 sheet: -2.02 (0.38), residues: 177 loop : -1.22 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.002 0.001 HIS A 163 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 0.03270 ( 431) hydrogen bonds : angle 4.62657 ( 1238) covalent geometry : bond 0.00242 ( 8889) covalent geometry : angle 0.48953 (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 216 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8089 (tp) REVERT: C 72 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: C 81 ASP cc_start: 0.8411 (t0) cc_final: 0.7925 (t0) REVERT: C 188 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 224 ASP cc_start: 0.8324 (t70) cc_final: 0.8018 (t70) REVERT: C 234 TYR cc_start: 0.8638 (m-10) cc_final: 0.8319 (m-10) REVERT: D 74 MET cc_start: 0.6661 (mpp) cc_final: 0.6398 (mtt) REVERT: A 31 GLU cc_start: 0.7756 (tp30) cc_final: 0.7484 (tp30) REVERT: A 211 LEU cc_start: 0.8085 (mt) cc_final: 0.7802 (mt) REVERT: A 286 MET cc_start: 0.8409 (mmt) cc_final: 0.7727 (mmt) REVERT: A 289 MET cc_start: 0.8127 (ttt) cc_final: 0.7170 (ttt) REVERT: A 293 LEU cc_start: 0.8521 (mm) cc_final: 0.8148 (mm) REVERT: B 101 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7688 (mmtt) outliers start: 14 outliers final: 9 residues processed: 209 average time/residue: 0.5376 time to fit residues: 147.7471 Evaluate side-chains 212 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 109 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.129546 restraints weight = 37893.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.135040 restraints weight = 14508.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.138479 restraints weight = 7349.268| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 8889 Z= 0.131 Angle : 0.829 59.198 12057 Z= 0.485 Chirality : 0.037 0.136 1302 Planarity : 0.004 0.039 1565 Dihedral : 6.126 84.463 1236 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.41 % Allowed : 14.35 % Favored : 84.24 % 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: 0.15 (0.26), residues: 1070 helix: 2.00 (0.24), residues: 485 sheet: -2.02 (0.38), residues: 177 loop : -1.22 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 10 HIS 0.002 0.001 HIS A 163 PHE 0.017 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 431) hydrogen bonds : angle 4.63159 ( 1238) covalent geometry : bond 0.00295 ( 8889) covalent geometry : angle 0.82936 (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 215 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 72 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: C 81 ASP cc_start: 0.8422 (t0) cc_final: 0.7930 (t0) REVERT: C 188 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7735 (tp) REVERT: C 224 ASP cc_start: 0.8314 (t70) cc_final: 0.8008 (t70) REVERT: C 234 TYR cc_start: 0.8637 (m-10) cc_final: 0.8330 (m-10) REVERT: D 74 MET cc_start: 0.6654 (mpp) cc_final: 0.6399 (mtt) REVERT: D 220 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7155 (mm110) REVERT: A 31 GLU cc_start: 0.7753 (tp30) cc_final: 0.7481 (tp30) REVERT: A 211 LEU cc_start: 0.8084 (mt) cc_final: 0.7800 (mt) REVERT: A 286 MET cc_start: 0.8411 (mmt) cc_final: 0.7725 (mmt) REVERT: A 289 MET cc_start: 0.8128 (ttt) cc_final: 0.7161 (ttt) REVERT: A 293 LEU cc_start: 0.8522 (mm) cc_final: 0.8120 (mm) REVERT: B 101 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7692 (mmtt) outliers start: 13 outliers final: 8 residues processed: 207 average time/residue: 0.5507 time to fit residues: 150.8839 Evaluate side-chains 213 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 117 CYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 220 GLN 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: 0.7980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3516 r_free = 0.3516 target = 0.152608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.129446 restraints weight = 38561.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.134966 restraints weight = 14712.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.138412 restraints weight = 7437.140| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.346 8889 Z= 0.302 Angle : 1.046 58.915 12057 Z= 0.653 Chirality : 0.037 0.205 1302 Planarity : 0.004 0.062 1565 Dihedral : 6.123 84.461 1236 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.20 % Allowed : 14.35 % 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: 0.15 (0.26), residues: 1070 helix: 1.99 (0.24), residues: 485 sheet: -2.02 (0.38), residues: 177 loop : -1.22 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.002 0.000 HIS A 163 PHE 0.017 0.001 PHE A 276 TYR 0.010 0.001 TYR A 238 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 431) hydrogen bonds : angle 4.62859 ( 1238) covalent geometry : bond 0.00618 ( 8889) covalent geometry : angle 1.04631 (12057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6538.51 seconds wall clock time: 111 minutes 58.59 seconds (6718.59 seconds total)