Starting phenix.real_space_refine on Wed Feb 14 07:40:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2024/7uxu_26862_trim_updated.pdb" } resolution = 2.74 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= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 8 5.16 5 C 2852 2.51 5 N 744 2.21 5 O 896 1.98 5 H 4268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8776 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "B" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "D" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.54 Number of scatterers: 8776 At special positions: 0 Unit cell: (77.6, 64, 111.2, 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) S 8 16.00 P 8 15.00 O 896 8.00 N 744 7.00 C 2852 6.00 H 4268 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 - 3.50 Amino acid : False - 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: 6.65 Conformation dependent library (CDL) restraints added in 891.3 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.1% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.956A pdb=" N LYS A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 201' Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.543A pdb=" N GLY A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.820A pdb=" N VAL A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 197 through 201 removed outlier: 4.009A pdb=" N LYS B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.530A pdb=" N GLY B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.768A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.577A pdb=" N ASN C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.783A pdb=" N VAL C 265 " --> pdb=" O GLN C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.571A pdb=" N ASN D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.810A pdb=" N VAL D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.983A pdb=" N TYR A 190 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER A 140 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 192 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 193 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 137 through 140 removed outlier: 6.977A pdb=" N TYR B 190 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N SER B 140 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 192 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 193 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 137 through 140 removed outlier: 6.993A pdb=" N TYR C 190 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER C 140 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 192 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 193 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 137 through 140 removed outlier: 7.032A pdb=" N TYR D 190 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER D 140 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR D 192 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 193 " --> pdb=" O LEU D 224 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4268 1.03 - 1.22: 4 1.22 - 1.42: 1936 1.42 - 1.61: 2656 1.61 - 1.80: 16 Bond restraints: 8880 Sorted by residual: bond pdb=" O1 1O4 A 301 " pdb=" P 1O4 A 301 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O1 1O4 C 301 " pdb=" P 1O4 C 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" O1 1O4 D 301 " pdb=" P 1O4 D 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" O1 1O4 B 301 " pdb=" P 1O4 B 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" O 1O4 B 301 " pdb=" P 1O4 B 301 " ideal model delta sigma weight residual 1.647 1.593 0.054 2.00e-02 2.50e+03 7.41e+00 ... (remaining 8875 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.45: 605 107.45 - 114.12: 10330 114.12 - 120.79: 2834 120.79 - 127.46: 2182 127.46 - 134.13: 65 Bond angle restraints: 16016 Sorted by residual: angle pdb=" O 1O4 C 301 " pdb=" P 1O4 C 301 " pdb=" O1 1O4 C 301 " ideal model delta sigma weight residual 96.18 105.54 -9.36 3.00e+00 1.11e-01 9.74e+00 angle pdb=" N PRO A 225 " pdb=" CA PRO A 225 " pdb=" C PRO A 225 " ideal model delta sigma weight residual 111.68 116.75 -5.07 1.67e+00 3.59e-01 9.23e+00 angle pdb=" O 1O4 A 301 " pdb=" P 1O4 A 301 " pdb=" O1 1O4 A 301 " ideal model delta sigma weight residual 96.18 105.09 -8.91 3.00e+00 1.11e-01 8.81e+00 angle pdb=" N PRO C 225 " pdb=" CA PRO C 225 " pdb=" C PRO C 225 " ideal model delta sigma weight residual 111.68 116.51 -4.83 1.67e+00 3.59e-01 8.36e+00 angle pdb=" O 1O4 D 301 " pdb=" P 1O4 D 301 " pdb=" O1 1O4 D 301 " ideal model delta sigma weight residual 96.18 104.75 -8.57 3.00e+00 1.11e-01 8.16e+00 ... (remaining 16011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 3847 16.56 - 33.12: 245 33.12 - 49.68: 107 49.68 - 66.24: 62 66.24 - 82.80: 11 Dihedral angle restraints: 4272 sinusoidal: 2416 harmonic: 1856 Sorted by residual: dihedral pdb=" CA MET B 222 " pdb=" C MET B 222 " pdb=" N ILE B 223 " pdb=" CA ILE B 223 " ideal model delta harmonic sigma weight residual -180.00 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA MET D 222 " pdb=" C MET D 222 " pdb=" N ILE D 223 " pdb=" CA ILE D 223 " ideal model delta harmonic sigma weight residual 180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA MET C 222 " pdb=" C MET C 222 " pdb=" N ILE C 223 " pdb=" CA ILE C 223 " ideal model delta harmonic sigma weight residual 180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 4269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 432 0.043 - 0.085: 215 0.085 - 0.128: 41 0.128 - 0.171: 20 0.171 - 0.214: 8 Chirality restraints: 716 Sorted by residual: chirality pdb=" C1 1O4 C 301 " pdb=" C 1O4 C 301 " pdb=" C2 1O4 C 301 " pdb=" O12 1O4 C 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 1O4 B 301 " pdb=" C 1O4 B 301 " pdb=" C2 1O4 B 301 " pdb=" O12 1O4 B 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 1O4 A 301 " pdb=" C 1O4 A 301 " pdb=" C2 1O4 A 301 " pdb=" O12 1O4 A 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 713 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C 1O4 B 301 " -0.369 2.00e-02 2.50e+03 1.47e-01 6.53e+02 pdb=" C15 1O4 B 301 " 0.121 2.00e-02 2.50e+03 pdb=" C16 1O4 B 301 " 0.089 2.00e-02 2.50e+03 pdb=" C17 1O4 B 301 " 0.035 2.00e-02 2.50e+03 pdb=" C18 1O4 B 301 " -0.111 2.00e-02 2.50e+03 pdb=" C19 1O4 B 301 " -0.171 2.00e-02 2.50e+03 pdb=" C20 1O4 B 301 " -0.073 2.00e-02 2.50e+03 pdb=" C21 1O4 B 301 " 0.052 2.00e-02 2.50e+03 pdb=" C22 1O4 B 301 " 0.110 2.00e-02 2.50e+03 pdb=" C23 1O4 B 301 " 0.153 2.00e-02 2.50e+03 pdb=" N5 1O4 B 301 " 0.047 2.00e-02 2.50e+03 pdb=" N6 1O4 B 301 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C 1O4 C 301 " 0.351 2.00e-02 2.50e+03 1.41e-01 5.94e+02 pdb=" C15 1O4 C 301 " -0.111 2.00e-02 2.50e+03 pdb=" C16 1O4 C 301 " -0.085 2.00e-02 2.50e+03 pdb=" C17 1O4 C 301 " -0.034 2.00e-02 2.50e+03 pdb=" C18 1O4 C 301 " 0.108 2.00e-02 2.50e+03 pdb=" C19 1O4 C 301 " 0.164 2.00e-02 2.50e+03 pdb=" C20 1O4 C 301 " 0.070 2.00e-02 2.50e+03 pdb=" C21 1O4 C 301 " -0.052 2.00e-02 2.50e+03 pdb=" C22 1O4 C 301 " -0.106 2.00e-02 2.50e+03 pdb=" C23 1O4 C 301 " -0.145 2.00e-02 2.50e+03 pdb=" N5 1O4 C 301 " -0.045 2.00e-02 2.50e+03 pdb=" N6 1O4 C 301 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C 1O4 A 301 " -0.347 2.00e-02 2.50e+03 1.39e-01 5.81e+02 pdb=" C15 1O4 A 301 " 0.104 2.00e-02 2.50e+03 pdb=" C16 1O4 A 301 " 0.082 2.00e-02 2.50e+03 pdb=" C17 1O4 A 301 " 0.034 2.00e-02 2.50e+03 pdb=" C18 1O4 A 301 " -0.107 2.00e-02 2.50e+03 pdb=" C19 1O4 A 301 " -0.163 2.00e-02 2.50e+03 pdb=" C20 1O4 A 301 " -0.068 2.00e-02 2.50e+03 pdb=" C21 1O4 A 301 " 0.051 2.00e-02 2.50e+03 pdb=" C22 1O4 A 301 " 0.105 2.00e-02 2.50e+03 pdb=" C23 1O4 A 301 " 0.146 2.00e-02 2.50e+03 pdb=" N5 1O4 A 301 " 0.046 2.00e-02 2.50e+03 pdb=" N6 1O4 A 301 " 0.117 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 940 2.27 - 2.85: 18841 2.85 - 3.43: 20497 3.43 - 4.02: 29577 4.02 - 4.60: 45215 Nonbonded interactions: 115070 Sorted by model distance: nonbonded pdb=" HG SER A 140 " pdb=" OE1 GLU A 208 " model vdw 1.686 1.850 nonbonded pdb=" HG SER B 140 " pdb=" OE1 GLU B 208 " model vdw 1.696 1.850 nonbonded pdb=" HG SER C 140 " pdb=" OE1 GLU C 208 " model vdw 1.709 1.850 nonbonded pdb=" HG SER D 140 " pdb=" OE1 GLU D 208 " model vdw 1.732 1.850 nonbonded pdb=" HE ARG A 178 " pdb=" OD1 ASP C 210 " model vdw 1.790 1.850 ... (remaining 115065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 5.820 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.600 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 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 : 0.007 0.057 4612 Z= 0.407 Angle : 1.006 9.361 6292 Z= 0.565 Chirality : 0.056 0.214 716 Planarity : 0.013 0.147 768 Dihedral : 17.352 82.799 1844 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -0.46 (0.34), residues: 528 helix: -0.82 (0.28), residues: 256 sheet: -0.19 (0.47), residues: 84 loop : 0.82 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 204 HIS 0.007 0.003 HIS C 228 PHE 0.019 0.003 PHE C 138 TYR 0.018 0.004 TYR D 238 ARG 0.013 0.002 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.736 Fit side-chains REVERT: A 189 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7524 (mtmt) REVERT: A 222 MET cc_start: 0.8702 (mtp) cc_final: 0.8450 (mtp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 2.7951 time to fit residues: 190.9699 Evaluate side-chains 46 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN C 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4612 Z= 0.206 Angle : 0.593 4.973 6292 Z= 0.315 Chirality : 0.041 0.145 716 Planarity : 0.004 0.032 768 Dihedral : 13.281 71.643 800 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.24 % Allowed : 7.64 % Favored : 91.12 % 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 (0.34), residues: 528 helix: 0.55 (0.32), residues: 248 sheet: -1.07 (0.44), residues: 84 loop : 0.02 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 204 HIS 0.005 0.002 HIS D 228 PHE 0.009 0.002 PHE C 138 TYR 0.014 0.002 TYR D 207 ARG 0.002 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.782 Fit side-chains REVERT: A 189 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7467 (mtmt) REVERT: A 222 MET cc_start: 0.8669 (mtp) cc_final: 0.8405 (mtp) REVERT: C 189 LYS cc_start: 0.7945 (mttt) cc_final: 0.7584 (mtmt) outliers start: 6 outliers final: 1 residues processed: 52 average time/residue: 2.5016 time to fit residues: 135.3850 Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.0010 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4612 Z= 0.115 Angle : 0.450 4.009 6292 Z= 0.240 Chirality : 0.038 0.136 716 Planarity : 0.003 0.025 768 Dihedral : 12.039 65.537 800 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.41 % Allowed : 10.33 % Favored : 89.26 % 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: 0.52 (0.35), residues: 528 helix: 1.40 (0.34), residues: 240 sheet: -1.31 (0.43), residues: 84 loop : -0.04 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 204 HIS 0.002 0.001 HIS A 141 PHE 0.005 0.001 PHE B 199 TYR 0.013 0.001 TYR C 207 ARG 0.001 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.853 Fit side-chains REVERT: A 155 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6761 (mp0) REVERT: A 189 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7426 (mtmt) REVERT: C 189 LYS cc_start: 0.7890 (mttt) cc_final: 0.7496 (mtmt) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 2.8001 time to fit residues: 133.5710 Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4612 Z= 0.247 Angle : 0.600 4.582 6292 Z= 0.312 Chirality : 0.043 0.149 716 Planarity : 0.004 0.034 768 Dihedral : 13.399 73.330 800 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.03 % Allowed : 11.78 % Favored : 87.19 % 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: -0.17 (0.34), residues: 528 helix: 0.93 (0.32), residues: 244 sheet: -1.82 (0.43), residues: 84 loop : -0.48 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 204 HIS 0.006 0.002 HIS B 228 PHE 0.010 0.002 PHE D 138 TYR 0.012 0.002 TYR D 207 ARG 0.003 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.849 Fit side-chains REVERT: A 189 LYS cc_start: 0.7888 (mmmm) cc_final: 0.7608 (mtmt) REVERT: C 189 LYS cc_start: 0.8052 (mttt) cc_final: 0.7650 (mtmt) outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 2.7311 time to fit residues: 119.3454 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4612 Z= 0.229 Angle : 0.572 4.444 6292 Z= 0.298 Chirality : 0.042 0.145 716 Planarity : 0.004 0.035 768 Dihedral : 13.157 72.177 800 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.41 % Allowed : 12.40 % Favored : 87.19 % 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: -0.43 (0.33), residues: 528 helix: 0.96 (0.32), residues: 236 sheet: -2.04 (0.42), residues: 84 loop : -0.86 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 204 HIS 0.004 0.001 HIS A 228 PHE 0.009 0.002 PHE D 138 TYR 0.012 0.002 TYR C 207 ARG 0.003 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6770 (mp0) REVERT: A 189 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7630 (mtmt) REVERT: C 189 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7709 (mtmt) REVERT: D 189 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7569 (tttt) REVERT: D 233 ASN cc_start: 0.8571 (m-40) cc_final: 0.8335 (m-40) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 2.8273 time to fit residues: 111.5671 Evaluate side-chains 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4612 Z= 0.272 Angle : 0.615 4.570 6292 Z= 0.318 Chirality : 0.043 0.149 716 Planarity : 0.005 0.037 768 Dihedral : 13.543 73.980 800 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.62 % Allowed : 12.81 % Favored : 86.57 % 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: -0.74 (0.33), residues: 528 helix: 0.76 (0.32), residues: 236 sheet: -2.24 (0.42), residues: 84 loop : -1.07 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 204 HIS 0.004 0.001 HIS A 228 PHE 0.010 0.002 PHE B 138 TYR 0.012 0.002 TYR C 207 ARG 0.003 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7670 (mtmt) REVERT: C 189 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7723 (mtmt) REVERT: D 189 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7607 (tttt) REVERT: D 233 ASN cc_start: 0.8595 (m-40) cc_final: 0.8370 (m-40) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 2.7881 time to fit residues: 110.1745 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 147 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4612 Z= 0.201 Angle : 0.540 4.317 6292 Z= 0.282 Chirality : 0.041 0.144 716 Planarity : 0.004 0.037 768 Dihedral : 12.894 70.897 800 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.41 % Allowed : 13.02 % Favored : 86.57 % 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: -0.53 (0.34), residues: 528 helix: 1.03 (0.33), residues: 236 sheet: -2.29 (0.42), residues: 84 loop : -1.02 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 204 HIS 0.003 0.001 HIS A 228 PHE 0.008 0.002 PHE A 138 TYR 0.013 0.002 TYR C 207 ARG 0.003 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6763 (mp0) REVERT: A 189 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7663 (mtmt) REVERT: C 189 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: D 189 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7588 (tttt) REVERT: D 233 ASN cc_start: 0.8599 (m-40) cc_final: 0.8343 (m-40) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 2.7931 time to fit residues: 101.7965 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4612 Z= 0.142 Angle : 0.470 3.894 6292 Z= 0.248 Chirality : 0.039 0.139 716 Planarity : 0.004 0.033 768 Dihedral : 12.076 67.114 800 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.41 % Allowed : 13.64 % Favored : 85.95 % 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: -0.09 (0.35), residues: 528 helix: 1.53 (0.34), residues: 236 sheet: -2.27 (0.42), residues: 84 loop : -0.87 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 204 HIS 0.002 0.001 HIS A 228 PHE 0.006 0.001 PHE A 138 TYR 0.012 0.001 TYR C 207 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6770 (mp0) REVERT: A 189 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7623 (mtmt) REVERT: C 189 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7702 (mtmt) REVERT: D 189 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7555 (tttt) REVERT: D 233 ASN cc_start: 0.8590 (m-40) cc_final: 0.8344 (m-40) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 2.5679 time to fit residues: 104.4554 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4612 Z= 0.184 Angle : 0.515 4.052 6292 Z= 0.269 Chirality : 0.040 0.143 716 Planarity : 0.004 0.033 768 Dihedral : 12.620 70.072 800 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.41 % Allowed : 13.43 % Favored : 86.16 % 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: -0.20 (0.35), residues: 528 helix: 1.42 (0.34), residues: 236 sheet: -2.33 (0.42), residues: 84 loop : -0.89 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 204 HIS 0.003 0.001 HIS A 228 PHE 0.008 0.002 PHE D 138 TYR 0.013 0.002 TYR C 207 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6750 (mp0) REVERT: A 189 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7647 (mtmt) REVERT: C 189 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7718 (mtmt) REVERT: D 189 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7581 (tttt) REVERT: D 233 ASN cc_start: 0.8597 (m-40) cc_final: 0.8351 (m-40) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 2.6680 time to fit residues: 105.5036 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4612 Z= 0.259 Angle : 0.595 4.399 6292 Z= 0.307 Chirality : 0.043 0.148 716 Planarity : 0.004 0.037 768 Dihedral : 13.327 73.492 800 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.41 % Allowed : 13.43 % Favored : 86.16 % 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: -0.56 (0.34), residues: 528 helix: 1.06 (0.33), residues: 236 sheet: -2.42 (0.42), residues: 84 loop : -1.05 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 204 HIS 0.004 0.001 HIS A 228 PHE 0.010 0.002 PHE D 138 TYR 0.012 0.002 TYR C 207 ARG 0.003 0.001 ARG B 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7687 (mtmt) REVERT: C 189 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7768 (mtmt) REVERT: D 189 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7624 (tttt) REVERT: D 233 ASN cc_start: 0.8598 (m-40) cc_final: 0.8357 (m-40) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 2.8773 time to fit residues: 104.7862 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100768 restraints weight = 16693.203| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.56 r_work: 0.3153 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4612 Z= 0.122 Angle : 0.444 4.137 6292 Z= 0.235 Chirality : 0.038 0.137 716 Planarity : 0.003 0.031 768 Dihedral : 11.777 65.306 800 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.41 % Allowed : 13.84 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.36), residues: 528 helix: 1.79 (0.34), residues: 236 sheet: -2.29 (0.42), residues: 84 loop : -0.75 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 204 HIS 0.001 0.000 HIS C 220 PHE 0.005 0.001 PHE B 149 TYR 0.012 0.001 TYR C 207 ARG 0.002 0.000 ARG A 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.15 seconds wall clock time: 63 minutes 29.24 seconds (3809.24 seconds total)