Starting phenix.real_space_refine on Thu Jan 18 14:26:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/01_2024/7uxu_26862_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/01_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_26862/01_2024/7uxu_26862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/01_2024/7uxu_26862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/01_2024/7uxu_26862_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/01_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.15, per 1000 atoms: 0.47 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: 6.61 Conformation dependent library (CDL) restraints added in 876.3 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: 1.43 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: 2.82 Time building geometry restraints manager: 6.84 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: 3822 16.56 - 33.12: 238 33.12 - 49.68: 102 49.68 - 66.24: 51 66.24 - 82.80: 11 Dihedral angle restraints: 4224 sinusoidal: 2368 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 4221 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 5.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.460 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- 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 : 0.776 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: 2.7752 time to fit residues: 189.6407 Evaluate side-chains 46 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.5980 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: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8661 moved from start: 0.1852 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= 0.191 Angle : 0.583 5.023 6292 Z= 0.309 Chirality : 0.041 0.144 716 Planarity : 0.004 0.030 768 Dihedral : 13.435 72.050 800 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.83 % Allowed : 7.85 % Favored : 91.32 % 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: 0.08 (0.34), residues: 528 helix: 0.61 (0.32), residues: 248 sheet: -1.07 (0.44), residues: 84 loop : 0.11 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 204 HIS 0.005 0.001 HIS D 228 PHE 0.009 0.002 PHE D 138 TYR 0.014 0.002 TYR D 207 ARG 0.002 0.000 ARG B 215 *********************** 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 51 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.718 Fit side-chains REVERT: A 189 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7420 (mtmt) REVERT: A 222 MET cc_start: 0.8664 (mtp) cc_final: 0.8454 (mtp) REVERT: C 189 LYS cc_start: 0.7931 (mttt) cc_final: 0.7571 (mtmt) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 2.5442 time to fit residues: 132.3661 Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 0.0370 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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: 0.8612 moved from start: 0.2396 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= 0.118 Angle : 0.454 3.964 6292 Z= 0.241 Chirality : 0.038 0.137 716 Planarity : 0.003 0.024 768 Dihedral : 12.042 65.637 800 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.24 % Allowed : 9.30 % Favored : 89.46 % 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: 0.57 (0.35), residues: 528 helix: 1.45 (0.34), residues: 240 sheet: -1.36 (0.43), residues: 84 loop : 0.01 (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 D 228 PHE 0.005 0.001 PHE B 199 TYR 0.013 0.001 TYR D 207 ARG 0.001 0.000 ARG D 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 52 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7438 (mtmt) REVERT: B 217 MET cc_start: 0.8751 (mmp) cc_final: 0.8125 (mmp) REVERT: C 189 LYS cc_start: 0.7883 (mttt) cc_final: 0.7490 (mtmt) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 2.6865 time to fit residues: 142.1888 Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 257 GLU 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: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 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: 2.7990 ------------------------------------------------------------------------------- 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: 0.8715 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4612 Z= 0.274 Angle : 0.629 4.638 6292 Z= 0.326 Chirality : 0.044 0.151 716 Planarity : 0.005 0.036 768 Dihedral : 13.622 74.291 800 Min Nonbonded Distance : 2.334 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: -0.28 (0.34), residues: 528 helix: 0.83 (0.32), residues: 244 sheet: -1.87 (0.43), residues: 84 loop : -0.51 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 204 HIS 0.006 0.002 HIS B 228 PHE 0.010 0.002 PHE D 138 TYR 0.011 0.002 TYR C 207 ARG 0.004 0.001 ARG B 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 : 0.790 Fit side-chains REVERT: A 189 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7620 (mtmt) REVERT: C 189 LYS cc_start: 0.8052 (mttt) cc_final: 0.7655 (mtmt) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 2.6470 time to fit residues: 115.6646 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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: 0.8709 moved from start: 0.2684 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= 0.223 Angle : 0.566 4.344 6292 Z= 0.295 Chirality : 0.042 0.146 716 Planarity : 0.004 0.037 768 Dihedral : 13.096 71.808 800 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 (0.34), residues: 528 helix: 0.93 (0.32), residues: 236 sheet: -2.06 (0.43), residues: 84 loop : -0.81 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 204 HIS 0.004 0.001 HIS A 228 PHE 0.009 0.002 PHE B 138 TYR 0.013 0.002 TYR C 207 ARG 0.004 0.001 ARG A 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 : 0.767 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7627 (mtmt) REVERT: C 189 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: D 189 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7544 (tttt) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 2.7871 time to fit residues: 110.0351 Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 264 ASP 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: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8740 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4612 Z= 0.312 Angle : 0.657 4.676 6292 Z= 0.338 Chirality : 0.045 0.152 716 Planarity : 0.005 0.042 768 Dihedral : 13.847 75.238 800 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.83 % Allowed : 12.19 % Favored : 86.98 % 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: -0.87 (0.33), residues: 528 helix: 0.61 (0.32), residues: 236 sheet: -2.28 (0.43), residues: 84 loop : -1.08 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 204 HIS 0.005 0.001 HIS A 228 PHE 0.011 0.002 PHE B 138 TYR 0.011 0.002 TYR C 207 ARG 0.004 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 43 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7681 (mtmt) REVERT: C 189 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7745 (mtmt) REVERT: D 189 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7601 (tttt) REVERT: D 233 ASN cc_start: 0.8601 (m-40) cc_final: 0.8375 (m-40) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 2.8184 time to fit residues: 117.4381 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 257 GLU 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: 4.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8694 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4612 Z= 0.164 Angle : 0.504 4.111 6292 Z= 0.265 Chirality : 0.040 0.142 716 Planarity : 0.004 0.036 768 Dihedral : 12.520 68.796 800 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.41 % Allowed : 12.60 % Favored : 86.98 % 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: -0.42 (0.34), residues: 528 helix: 1.14 (0.33), residues: 236 sheet: -2.30 (0.43), residues: 84 loop : -0.95 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 204 HIS 0.002 0.001 HIS A 228 PHE 0.007 0.001 PHE B 138 TYR 0.013 0.002 TYR C 207 ARG 0.002 0.000 ARG C 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 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6755 (mp0) REVERT: A 189 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7632 (mtmt) REVERT: C 189 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7714 (mtmt) REVERT: D 189 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7556 (tttt) REVERT: D 233 ASN cc_start: 0.8577 (m-40) cc_final: 0.8335 (m-40) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 2.6805 time to fit residues: 100.6038 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 264 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 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: 1.3184 ------------------------------------------------------------------------------- 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: 0.8682 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4612 Z= 0.153 Angle : 0.481 4.005 6292 Z= 0.252 Chirality : 0.039 0.140 716 Planarity : 0.004 0.033 768 Dihedral : 12.178 67.721 800 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.21 % Allowed : 13.02 % Favored : 86.78 % 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: -0.11 (0.35), residues: 528 helix: 1.51 (0.34), residues: 236 sheet: -2.30 (0.42), residues: 84 loop : -0.86 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 204 HIS 0.002 0.001 HIS A 228 PHE 0.007 0.001 PHE D 138 TYR 0.013 0.002 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: 1 poor density : 40 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6774 (mp0) REVERT: A 189 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7632 (mtmt) REVERT: C 189 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7702 (mtmt) REVERT: D 189 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7556 (tttt) REVERT: D 233 ASN cc_start: 0.8586 (m-40) cc_final: 0.8343 (m-40) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 2.5354 time to fit residues: 105.7497 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.8696 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4612 Z= 0.177 Angle : 0.510 4.060 6292 Z= 0.266 Chirality : 0.040 0.142 716 Planarity : 0.004 0.033 768 Dihedral : 12.552 69.753 800 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.21 % Allowed : 13.22 % 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: -0.18 (0.35), residues: 528 helix: 1.43 (0.34), residues: 236 sheet: -2.36 (0.42), residues: 84 loop : -0.85 (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 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6756 (mp0) REVERT: A 189 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7646 (mtmt) REVERT: C 189 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7716 (mtmt) REVERT: D 189 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7565 (tttt) REVERT: D 233 ASN cc_start: 0.8598 (m-40) cc_final: 0.8359 (m-40) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 2.6020 time to fit residues: 103.1858 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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: 0.8648 moved from start: 0.3068 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= 0.116 Angle : 0.435 4.174 6292 Z= 0.229 Chirality : 0.038 0.136 716 Planarity : 0.003 0.028 768 Dihedral : 11.542 64.630 800 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.21 % Allowed : 13.43 % Favored : 86.36 % 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: 0.38 (0.36), residues: 528 helix: 1.99 (0.35), residues: 236 sheet: -2.19 (0.43), residues: 84 loop : -0.65 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 165 HIS 0.001 0.000 HIS D 220 PHE 0.005 0.001 PHE D 138 TYR 0.011 0.001 TYR C 207 ARG 0.002 0.000 ARG C 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6755 (mp0) REVERT: A 189 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7599 (mtmt) REVERT: B 155 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6641 (mp0) REVERT: C 189 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7655 (mtmt) REVERT: D 189 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7526 (tttt) REVERT: D 233 ASN cc_start: 0.8559 (m-40) cc_final: 0.8310 (m-40) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 2.5728 time to fit residues: 104.5067 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 264 ASP 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: 1.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.113145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102610 restraints weight = 16696.204| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.57 r_work: 0.3180 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4612 Z= 0.110 Angle : 0.419 4.089 6292 Z= 0.220 Chirality : 0.038 0.137 716 Planarity : 0.003 0.025 768 Dihedral : 11.055 62.589 800 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.21 % Allowed : 13.02 % Favored : 86.78 % 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: 0.82 (0.37), residues: 528 helix: 2.43 (0.35), residues: 236 sheet: -2.03 (0.44), residues: 84 loop : -0.48 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 165 HIS 0.001 0.000 HIS D 220 PHE 0.005 0.001 PHE A 138 TYR 0.012 0.001 TYR C 207 ARG 0.002 0.000 ARG C 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3456.26 seconds wall clock time: 61 minutes 12.27 seconds (3672.27 seconds total)