Starting phenix.real_space_refine (version: dev) on Sat Feb 18 14:42:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2023/7wju_32548_neut.pdb" } resolution = 2.69 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= -0.001 sd= 0.243 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 Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "B ASP 14": "OD1" <-> "OD2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8322 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3308 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1652 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 1 Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2845 Classifications: {'RNA': 133} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 55} Link IDs: {'rna2p': 19, 'rna3p': 113} Chain breaks: 3 Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 5.49, per 1000 atoms: 0.66 Number of scatterers: 8322 At special positions: 0 Unit cell: (81.8748, 99.1116, 117.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 158 15.00 O 1981 8.00 N 1510 7.00 C 4652 6.00 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: 4.00 Conformation dependent library (CDL) restraints added in 808.1 milliseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 46.8% alpha, 21.9% beta 64 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 56 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.683A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.505A pdb=" N TYR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.732A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.609A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.867A pdb=" N LEU A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'B' and resid 18 through 46 Processing helix chain 'B' and resid 50 through 55 removed outlier: 4.341A pdb=" N ASP B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.504A pdb=" N TYR B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.808A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 5.046A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.487A pdb=" N LEU A 218 " --> pdb=" O CYS A 318 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 320 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 220 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN A 322 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.594A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP B 201 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 11 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.594A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 186 " --> pdb=" O ASP B 208 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1209 1.32 - 1.45: 3199 1.45 - 1.57: 4059 1.57 - 1.69: 310 1.69 - 1.81: 37 Bond restraints: 8814 Sorted by residual: bond pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.23e-02 6.61e+03 9.80e+00 bond pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.59e+00 bond pdb=" O5' A C 90 " pdb=" C5' A C 90 " ideal model delta sigma weight residual 1.420 1.462 -0.042 1.50e-02 4.44e+03 7.67e+00 bond pdb=" O5' G C 117 " pdb=" C5' G C 117 " ideal model delta sigma weight residual 1.420 1.461 -0.041 1.50e-02 4.44e+03 7.58e+00 bond pdb=" O5' C C 118 " pdb=" C5' C C 118 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.71e+00 ... (remaining 8809 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.16: 365 103.16 - 110.91: 3728 110.91 - 118.67: 3811 118.67 - 126.43: 4198 126.43 - 134.18: 537 Bond angle restraints: 12639 Sorted by residual: angle pdb=" O3' A C 89 " pdb=" C3' A C 89 " pdb=" C2' A C 89 " ideal model delta sigma weight residual 113.70 98.54 15.16 1.50e+00 4.44e-01 1.02e+02 angle pdb=" O3' A C 91 " pdb=" P C C 92 " pdb=" O5' C C 92 " ideal model delta sigma weight residual 104.00 95.40 8.60 1.50e+00 4.44e-01 3.29e+01 angle pdb=" N LEU A 337 " pdb=" CA LEU A 337 " pdb=" C LEU A 337 " ideal model delta sigma weight residual 110.80 98.91 11.89 2.13e+00 2.20e-01 3.12e+01 angle pdb=" O5' A C 91 " pdb=" C5' A C 91 " pdb=" C4' A C 91 " ideal model delta sigma weight residual 111.70 104.43 7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" C ILE A 329 " pdb=" N ARG A 330 " pdb=" CA ARG A 330 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+01 ... (remaining 12634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4606 33.86 - 67.73: 283 67.73 - 101.59: 12 101.59 - 135.46: 0 135.46 - 169.32: 2 Dihedral angle restraints: 4903 sinusoidal: 3121 harmonic: 1782 Sorted by residual: dihedral pdb=" O4' U C 75 " pdb=" C1' U C 75 " pdb=" N1 U C 75 " pdb=" C2 U C 75 " ideal model delta sinusoidal sigma weight residual -160.00 9.32 -169.32 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CA GLY B 47 " pdb=" C GLY B 47 " pdb=" N PHE B 48 " pdb=" CA PHE B 48 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLN A 191 " pdb=" C GLN A 191 " pdb=" N ILE A 192 " pdb=" CA ILE A 192 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 4900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1333 0.096 - 0.192: 133 0.192 - 0.289: 12 0.289 - 0.385: 3 0.385 - 0.481: 12 Chirality restraints: 1493 Sorted by residual: chirality pdb=" P A C 90 " pdb=" OP1 A C 90 " pdb=" OP2 A C 90 " pdb=" O5' A C 90 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" P U C 75 " pdb=" OP1 U C 75 " pdb=" OP2 U C 75 " pdb=" O5' U C 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 1490 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 117 " 0.050 2.00e-02 2.50e+03 1.98e-02 1.17e+01 pdb=" N9 G C 117 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G C 117 " -0.016 2.00e-02 2.50e+03 pdb=" N7 G C 117 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G C 117 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G C 117 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G C 117 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G C 117 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G C 117 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 117 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 117 " -0.023 2.00e-02 2.50e+03 pdb=" C4 G C 117 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 173 " -0.045 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 U C 173 " 0.040 2.00e-02 2.50e+03 pdb=" C2 U C 173 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U C 173 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U C 173 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 173 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U C 173 " -0.014 2.00e-02 2.50e+03 pdb=" C5 U C 173 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U C 173 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 174 " -0.043 2.00e-02 2.50e+03 1.74e-02 9.09e+00 pdb=" N9 G C 174 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G C 174 " 0.022 2.00e-02 2.50e+03 pdb=" N7 G C 174 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 174 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G C 174 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G C 174 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G C 174 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G C 174 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G C 174 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G C 174 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G C 174 " -0.001 2.00e-02 2.50e+03 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2436 2.84 - 3.36: 6488 3.36 - 3.87: 16453 3.87 - 4.39: 18912 4.39 - 4.90: 27169 Nonbonded interactions: 71458 Sorted by model distance: nonbonded pdb=" O ASN A 302 " pdb=" OG SER A 306 " model vdw 2.325 2.440 nonbonded pdb=" O3' A C 89 " pdb=" O2' A C 89 " model vdw 2.332 2.432 nonbonded pdb=" N ILE B 2 " pdb=" O TYR B 207 " model vdw 2.337 2.520 nonbonded pdb=" O TYR A 84 " pdb=" OG SER A 150 " model vdw 2.378 2.440 nonbonded pdb=" O2' A C 20 " pdb=" OP2 A C 22 " model vdw 2.384 2.440 ... (remaining 71453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 21 5.16 5 C 4652 2.51 5 N 1510 2.21 5 O 1981 1.98 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: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.110 Process input model: 28.610 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.076 8814 Z= 0.452 Angle : 0.988 15.161 12639 Z= 0.549 Chirality : 0.070 0.481 1493 Planarity : 0.006 0.057 1027 Dihedral : 17.675 169.321 3761 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % 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: -2.47 (0.29), residues: 599 helix: -1.37 (0.26), residues: 280 sheet: -0.65 (0.42), residues: 124 loop : -2.46 (0.36), residues: 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.717 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.6288 time to fit residues: 157.3490 Evaluate side-chains 66 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 106 GLN A 252 ASN A 303 HIS A 322 GLN A 412 ASN B 26 GLN B 72 HIS B 87 ASN B 93 GLN B 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8814 Z= 0.220 Angle : 0.597 6.037 12639 Z= 0.328 Chirality : 0.042 0.191 1493 Planarity : 0.005 0.043 1027 Dihedral : 17.576 177.997 2512 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer Outliers : 2.07 % 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: -0.97 (0.32), residues: 599 helix: 0.26 (0.29), residues: 291 sheet: -0.25 (0.43), residues: 123 loop : -2.30 (0.38), residues: 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.626 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 1.4254 time to fit residues: 108.6192 Evaluate side-chains 64 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1987 time to fit residues: 1.1683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 26 GLN B 40 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 8814 Z= 0.476 Angle : 0.761 8.649 12639 Z= 0.407 Chirality : 0.051 0.227 1493 Planarity : 0.006 0.050 1027 Dihedral : 17.889 178.504 2512 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.33 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.61 (0.32), residues: 599 helix: 0.70 (0.30), residues: 285 sheet: -0.16 (0.42), residues: 124 loop : -2.25 (0.38), residues: 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.712 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 1.4423 time to fit residues: 121.9055 Evaluate side-chains 76 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.5377 time to fit residues: 2.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 194 HIS B 26 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8814 Z= 0.197 Angle : 0.567 6.290 12639 Z= 0.310 Chirality : 0.040 0.179 1493 Planarity : 0.004 0.045 1027 Dihedral : 17.539 178.705 2512 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.02 (0.34), residues: 599 helix: 1.18 (0.31), residues: 292 sheet: -0.08 (0.42), residues: 130 loop : -1.96 (0.42), residues: 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.726 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.3278 time to fit residues: 97.4941 Evaluate side-chains 66 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.8660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 26 GLN B 40 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8814 Z= 0.249 Angle : 0.593 6.072 12639 Z= 0.322 Chirality : 0.042 0.193 1493 Planarity : 0.004 0.044 1027 Dihedral : 17.560 178.191 2512 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.34), residues: 599 helix: 1.46 (0.31), residues: 286 sheet: 0.08 (0.42), residues: 131 loop : -1.81 (0.43), residues: 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.745 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 1.2895 time to fit residues: 93.6974 Evaluate side-chains 68 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 1.2801 time to fit residues: 6.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 26 GLN B 131 ASN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8814 Z= 0.174 Angle : 0.540 6.030 12639 Z= 0.294 Chirality : 0.039 0.175 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.391 178.587 2512 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 599 helix: 1.72 (0.31), residues: 286 sheet: 0.17 (0.43), residues: 130 loop : -1.67 (0.44), residues: 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.632 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 1.3134 time to fit residues: 93.7531 Evaluate side-chains 67 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0762 time to fit residues: 1.0446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8814 Z= 0.227 Angle : 0.570 6.036 12639 Z= 0.309 Chirality : 0.040 0.187 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.426 178.302 2512 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.88 % 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: 0.61 (0.35), residues: 599 helix: 1.75 (0.31), residues: 286 sheet: 0.21 (0.42), residues: 131 loop : -1.64 (0.44), residues: 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.795 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 1.1925 time to fit residues: 90.4984 Evaluate side-chains 65 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.1167 time to fit residues: 2.1107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 131 ASN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 8814 Z= 0.382 Angle : 0.678 7.656 12639 Z= 0.364 Chirality : 0.046 0.215 1493 Planarity : 0.005 0.044 1027 Dihedral : 17.654 178.285 2512 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.33 (0.34), residues: 599 helix: 1.48 (0.31), residues: 285 sheet: 0.27 (0.43), residues: 124 loop : -1.79 (0.42), residues: 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.850 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 1.3280 time to fit residues: 103.0617 Evaluate side-chains 72 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.0301 time to fit residues: 3.1516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 412 ASN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8814 Z= 0.223 Angle : 0.579 6.178 12639 Z= 0.314 Chirality : 0.041 0.191 1493 Planarity : 0.004 0.044 1027 Dihedral : 17.455 178.666 2512 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.35), residues: 599 helix: 1.64 (0.31), residues: 286 sheet: 0.16 (0.42), residues: 131 loop : -1.62 (0.45), residues: 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.782 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 1.2124 time to fit residues: 86.6062 Evaluate side-chains 65 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.7828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 26 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8814 Z= 0.298 Angle : 0.619 6.032 12639 Z= 0.335 Chirality : 0.043 0.201 1493 Planarity : 0.004 0.044 1027 Dihedral : 17.537 178.317 2512 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 599 helix: 1.59 (0.31), residues: 285 sheet: 0.12 (0.42), residues: 131 loop : -1.71 (0.44), residues: 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.657 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 69 average time/residue: 1.2697 time to fit residues: 93.3242 Evaluate side-chains 70 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.1979 time to fit residues: 2.1572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 412 ASN B 26 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.180733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135123 restraints weight = 7595.019| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.06 r_work: 0.3266 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8814 Z= 0.167 Angle : 0.530 6.114 12639 Z= 0.288 Chirality : 0.038 0.173 1493 Planarity : 0.004 0.043 1027 Dihedral : 17.283 179.532 2512 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.69 % 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: 0.70 (0.35), residues: 599 helix: 1.83 (0.32), residues: 286 sheet: 0.14 (0.42), residues: 130 loop : -1.51 (0.45), residues: 183 =============================================================================== Job complete usr+sys time: 2432.32 seconds wall clock time: 44 minutes 39.90 seconds (2679.90 seconds total)