Starting phenix.real_space_refine (version: dev) on Sat Feb 18 21:49:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2023/7uxu_26862_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2023/7uxu_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_2023/7uxu_26862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2023/7uxu_26862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2023/7uxu_26862_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxu_26862/02_2023/7uxu_26862_trim_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 4.62, per 1000 atoms: 0.53 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: 7.17 Conformation dependent library (CDL) restraints added in 747.2 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: 0.55 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: 2.74 Time building geometry restraints manager: 7.34 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 - 12.84: 3131 12.84 - 25.67: 264 25.67 - 38.51: 67 38.51 - 51.35: 43 51.35 - 64.18: 23 Dihedral angle restraints: 3528 sinusoidal: 1672 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 3525 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 2.550 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: 0.130 Extract box with map and model: 6.250 Check model and map are aligned: 0.140 Process input model: 31.000 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 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 : 14.121 62.195 1668 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 % 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 *********************** 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 : 0.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 2.7795 time to fit residues: 189.9489 Evaluate side-chains 45 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9872 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8769 moved from start: 0.1961 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 : 0.574 5.026 6292 Z= 0.301 Chirality : 0.041 0.144 716 Planarity : 0.004 0.026 768 Dihedral : 8.239 39.870 624 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.03 % 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: 0.66 (0.32), residues: 248 sheet: -0.98 (0.45), residues: 84 loop : 0.18 (0.44), residues: 196 *********************** 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 52 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.815 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 2.6058 time to fit residues: 138.0597 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2379 time to fit residues: 1.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.0010 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.2438 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= 0.108 Angle : 0.454 4.314 6292 Z= 0.236 Chirality : 0.039 0.136 716 Planarity : 0.002 0.019 768 Dihedral : 7.389 37.413 624 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 0.83 % 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 (0.36), residues: 528 helix: 1.56 (0.34), residues: 240 sheet: -1.18 (0.44), residues: 84 loop : 0.09 (0.43), residues: 204 *********************** 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 45 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.769 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 2.4336 time to fit residues: 111.8725 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.3529 time to fit residues: 1.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8815 moved from start: 0.2492 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= 0.243 Angle : 0.603 4.823 6292 Z= 0.312 Chirality : 0.044 0.149 716 Planarity : 0.004 0.029 768 Dihedral : 8.028 40.147 624 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.03 % 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: 0.00 (0.34), residues: 528 helix: 1.08 (0.32), residues: 244 sheet: -1.76 (0.42), residues: 84 loop : -0.37 (0.42), residues: 200 *********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.703 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 2.6029 time to fit residues: 105.7601 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2584 time to fit residues: 1.6173 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.8805 moved from start: 0.2741 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= 0.188 Angle : 0.540 4.648 6292 Z= 0.279 Chirality : 0.042 0.142 716 Planarity : 0.004 0.030 768 Dihedral : 7.670 35.574 624 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.34), residues: 528 helix: 1.27 (0.33), residues: 236 sheet: -1.93 (0.42), residues: 84 loop : -0.65 (0.39), residues: 208 *********************** 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 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.845 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 2.7915 time to fit residues: 101.7883 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2323 time to fit residues: 1.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8776 moved from start: 0.2884 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= 0.133 Angle : 0.474 4.457 6292 Z= 0.244 Chirality : 0.040 0.137 716 Planarity : 0.003 0.025 768 Dihedral : 7.182 33.168 624 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.35), residues: 528 helix: 1.72 (0.34), residues: 236 sheet: -1.95 (0.42), residues: 84 loop : -0.62 (0.40), residues: 208 *********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.837 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 2.4919 time to fit residues: 96.4184 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.8312 time to fit residues: 3.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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: 0.8790 moved from start: 0.2920 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= 0.154 Angle : 0.497 4.521 6292 Z= 0.255 Chirality : 0.040 0.140 716 Planarity : 0.003 0.025 768 Dihedral : 7.245 33.308 624 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer Outliers : 0.62 % 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: 1.73 (0.34), residues: 236 sheet: -2.11 (0.42), residues: 84 loop : -0.68 (0.40), residues: 208 *********************** 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: 3 poor density : 35 time to evaluate : 0.805 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 2.4611 time to fit residues: 90.0167 Evaluate side-chains 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2314 time to fit residues: 1.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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: 0.8792 moved from start: 0.2953 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= 0.155 Angle : 0.498 4.510 6292 Z= 0.255 Chirality : 0.040 0.140 716 Planarity : 0.003 0.025 768 Dihedral : 7.212 32.334 624 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 0.41 % 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: 1.77 (0.34), residues: 236 sheet: -2.19 (0.42), residues: 84 loop : -0.69 (0.40), residues: 208 *********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.735 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 2.4352 time to fit residues: 96.7623 Evaluate side-chains 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2717 time to fit residues: 1.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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: 0.8793 moved from start: 0.2977 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= 0.156 Angle : 0.500 4.505 6292 Z= 0.256 Chirality : 0.041 0.140 716 Planarity : 0.003 0.025 768 Dihedral : 7.191 32.046 624 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.41 % 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: 0.21 (0.36), residues: 528 helix: 1.81 (0.34), residues: 236 sheet: -2.25 (0.43), residues: 84 loop : -0.70 (0.40), residues: 208 *********************** 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: 2 poor density : 37 time to evaluate : 0.806 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 2.6103 time to fit residues: 100.8751 Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2438 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8823 moved from start: 0.2936 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= 0.225 Angle : 0.572 4.768 6292 Z= 0.293 Chirality : 0.043 0.145 716 Planarity : 0.004 0.029 768 Dihedral : 7.590 33.611 624 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.35), residues: 528 helix: 1.40 (0.33), residues: 236 sheet: -2.35 (0.43), residues: 84 loop : -0.84 (0.39), residues: 208 ********************** 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 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.784 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 2.6438 time to fit residues: 102.1626 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2512 time to fit residues: 1.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.120155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110906 restraints weight = 16679.661| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.31 r_work: 0.3271 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 4612 Z= 0.123 Angle : 0.462 4.348 6292 Z= 0.238 Chirality : 0.039 0.137 716 Planarity : 0.003 0.024 768 Dihedral : 6.956 29.584 624 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.41 % 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: 0.39 (0.36), residues: 528 helix: 2.00 (0.35), residues: 236 sheet: -2.25 (0.42), residues: 84 loop : -0.63 (0.40), residues: 208 =============================================================================== Job complete usr+sys time: 3329.69 seconds wall clock time: 59 minutes 29.15 seconds (3569.15 seconds total)