Starting phenix.real_space_refine on Wed Feb 14 01:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2024/7wju_32548_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2024/7wju_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_2024/7wju_32548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2024/7wju_32548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2024/7wju_32548_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/02_2024/7wju_32548_neut.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 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. 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.51, 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: 4.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.69 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: 3.33 Time building geometry restraints manager: 4.42 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: 4860 33.86 - 67.73: 504 67.73 - 101.59: 43 101.59 - 135.46: 0 135.46 - 169.32: 2 Dihedral angle restraints: 5409 sinusoidal: 3627 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 5406 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 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.450 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 21.910 169.321 4267 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 % Allowed : 4.89 % Favored : 95.11 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 43 HIS 0.008 0.001 HIS A 303 PHE 0.015 0.003 PHE B 48 TYR 0.030 0.003 TYR A 233 ARG 0.004 0.000 ARG A 371 *********************** 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 : 0.760 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.5714 time to fit residues: 151.7275 Evaluate side-chains 66 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.1276 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= 0.219 Angle : 0.597 6.058 12639 Z= 0.328 Chirality : 0.042 0.195 1493 Planarity : 0.005 0.043 1027 Dihedral : 23.145 177.673 3018 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 12.22 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 599 helix: 0.27 (0.29), residues: 291 sheet: -0.25 (0.43), residues: 123 loop : -2.29 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.003 0.001 HIS A 303 PHE 0.014 0.002 PHE B 48 TYR 0.023 0.002 TYR A 351 ARG 0.003 0.000 ARG A 179 *********************** 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 : 0.757 Fit side-chains REVERT: A 155 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6856 (mt0) REVERT: A 218 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 30 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: B 137 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4382 (mpp) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 1.3630 time to fit residues: 103.9078 Evaluate side-chains 69 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 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: 7.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8814 Z= 0.458 Angle : 0.749 8.488 12639 Z= 0.402 Chirality : 0.050 0.223 1493 Planarity : 0.006 0.049 1027 Dihedral : 23.327 177.876 3018 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.34 % Favored : 95.49 % Rotamer: Outliers : 3.01 % Allowed : 11.65 % Favored : 85.34 % 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: -0.56 (0.33), residues: 599 helix: 0.74 (0.30), residues: 285 sheet: -0.15 (0.42), residues: 124 loop : -2.21 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 43 HIS 0.004 0.001 HIS A 278 PHE 0.018 0.003 PHE B 48 TYR 0.016 0.003 TYR A 5 ARG 0.004 0.001 ARG A 179 *********************** 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 88 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.740 Fit side-chains REVERT: A 155 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: A 254 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7265 (mtm-85) REVERT: B 30 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: B 44 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7356 (mt-10) outliers start: 16 outliers final: 5 residues processed: 80 average time/residue: 1.4685 time to fit residues: 124.5480 Evaluate side-chains 78 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 THR 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: 0.7980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.1539 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= 0.226 Angle : 0.592 6.063 12639 Z= 0.322 Chirality : 0.041 0.189 1493 Planarity : 0.004 0.045 1027 Dihedral : 23.122 177.853 3018 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.01 % Allowed : 12.41 % Favored : 84.59 % 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: 1.26 (0.31), residues: 285 sheet: -0.07 (0.41), residues: 131 loop : -1.91 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 PHE 0.012 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.002 0.000 ARG A 179 *********************** 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 81 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.655 Fit side-chains REVERT: A 155 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: A 218 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 254 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7439 (mtm-85) REVERT: B 30 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: B 44 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7350 (mt-10) outliers start: 16 outliers final: 7 residues processed: 72 average time/residue: 1.4765 time to fit residues: 112.9590 Evaluate side-chains 77 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 199 ASN 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: 0.7980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 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 B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1689 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 : 0.573 6.118 12639 Z= 0.311 Chirality : 0.040 0.188 1493 Planarity : 0.004 0.044 1027 Dihedral : 23.056 177.431 3018 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.44 % Allowed : 13.72 % Favored : 83.83 % 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: 0.36 (0.34), residues: 599 helix: 1.50 (0.31), residues: 287 sheet: 0.11 (0.42), residues: 131 loop : -1.71 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 72 PHE 0.013 0.002 PHE B 48 TYR 0.018 0.002 TYR A 351 ARG 0.002 0.000 ARG A 330 *********************** 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 80 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.740 Fit side-chains REVERT: A 155 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: A 218 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7994 (mm) REVERT: B 30 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 44 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7365 (mt-10) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 1.5491 time to fit residues: 117.5194 Evaluate side-chains 75 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 THR 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: 0.4980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8814 Z= 0.182 Angle : 0.545 6.061 12639 Z= 0.296 Chirality : 0.039 0.177 1493 Planarity : 0.004 0.042 1027 Dihedral : 22.988 177.842 3018 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.44 % Allowed : 13.91 % Favored : 83.65 % 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: 0.58 (0.35), residues: 599 helix: 1.70 (0.31), residues: 287 sheet: 0.18 (0.43), residues: 131 loop : -1.61 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS A 72 PHE 0.012 0.002 PHE B 48 TYR 0.019 0.001 TYR A 351 ARG 0.002 0.000 ARG B 6 *********************** 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 76 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.747 Fit side-chains REVERT: A 218 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8037 (mm) REVERT: B 30 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 44 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 208 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.6027 (m-30) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 1.5562 time to fit residues: 114.7881 Evaluate side-chains 73 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 208 ASP 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: 4.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7915 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8814 Z= 0.367 Angle : 0.672 7.456 12639 Z= 0.360 Chirality : 0.046 0.215 1493 Planarity : 0.005 0.044 1027 Dihedral : 23.169 177.366 3018 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.76 % Allowed : 13.72 % Favored : 82.52 % 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: 0.34 (0.34), residues: 599 helix: 1.51 (0.31), residues: 285 sheet: 0.27 (0.44), residues: 124 loop : -1.82 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.003 PHE A 102 TYR 0.016 0.002 TYR A 351 ARG 0.003 0.001 ARG A 330 *********************** 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 90 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.704 Fit side-chains REVERT: B 30 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: B 44 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: B 208 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.6049 (m-30) outliers start: 20 outliers final: 11 residues processed: 80 average time/residue: 1.3678 time to fit residues: 115.7585 Evaluate side-chains 79 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 208 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 93 GLN B 26 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8814 Z= 0.156 Angle : 0.530 6.060 12639 Z= 0.287 Chirality : 0.038 0.172 1493 Planarity : 0.004 0.043 1027 Dihedral : 22.934 179.103 3018 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 15.79 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.35), residues: 599 helix: 1.73 (0.31), residues: 291 sheet: 0.25 (0.42), residues: 131 loop : -1.67 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.002 0.001 HIS A 72 PHE 0.012 0.002 PHE A 102 TYR 0.017 0.001 TYR A 351 ARG 0.003 0.000 ARG B 25 *********************** 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 70 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.594 Fit side-chains REVERT: A 155 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: A 218 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 30 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7145 (mt-10) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 1.3201 time to fit residues: 91.1835 Evaluate side-chains 64 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 164 SER 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: 6.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 40 GLN B 131 ASN B 151 ASN B 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8814 Z= 0.399 Angle : 0.689 7.837 12639 Z= 0.367 Chirality : 0.047 0.217 1493 Planarity : 0.005 0.044 1027 Dihedral : 23.164 177.399 3018 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 15.60 % Favored : 81.95 % 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: 0.39 (0.34), residues: 599 helix: 1.54 (0.31), residues: 285 sheet: 0.33 (0.44), residues: 124 loop : -1.81 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 43 HIS 0.003 0.001 HIS A 278 PHE 0.014 0.003 PHE A 102 TYR 0.015 0.003 TYR A 5 ARG 0.004 0.001 ARG A 179 *********************** 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 77 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.767 Fit side-chains REVERT: A 218 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 323 MET cc_start: 0.8167 (ptt) cc_final: 0.7921 (ptt) REVERT: B 30 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: B 44 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7356 (mt-10) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 1.3336 time to fit residues: 97.8714 Evaluate side-chains 72 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8814 Z= 0.202 Angle : 0.565 6.084 12639 Z= 0.305 Chirality : 0.040 0.183 1493 Planarity : 0.004 0.044 1027 Dihedral : 23.022 178.009 3018 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.32 % Allowed : 17.67 % Favored : 81.02 % 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: 0.62 (0.35), residues: 599 helix: 1.74 (0.31), residues: 286 sheet: 0.21 (0.42), residues: 131 loop : -1.61 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 43 HIS 0.002 0.000 HIS A 77 PHE 0.012 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.002 0.000 ARG B 25 ********************** 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 69 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.685 Fit side-chains REVERT: A 218 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 323 MET cc_start: 0.8164 (ptt) cc_final: 0.7919 (ptt) REVERT: B 30 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7184 (mt-10) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 1.2638 time to fit residues: 88.7833 Evaluate side-chains 68 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.181995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137010 restraints weight = 7624.376| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.04 r_work: 0.3290 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8814 Z= 0.146 Angle : 0.531 6.076 12639 Z= 0.287 Chirality : 0.038 0.168 1493 Planarity : 0.003 0.042 1027 Dihedral : 22.953 178.851 3018 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.50 % Allowed : 17.11 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.35), residues: 599 helix: 1.96 (0.32), residues: 286 sheet: 0.17 (0.42), residues: 131 loop : -1.48 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS A 72 PHE 0.009 0.001 PHE A 102 TYR 0.016 0.001 TYR A 351 ARG 0.003 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.59 seconds wall clock time: 47 minutes 40.79 seconds (2860.79 seconds total)