Starting phenix.real_space_refine on Tue Nov 14 09:22:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/11_2023/7wju_32548_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/11_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_32548/11_2023/7wju_32548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/11_2023/7wju_32548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/11_2023/7wju_32548_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wju_32548/11_2023/7wju_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-1.21rc1-5144/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: 6.42, per 1000 atoms: 0.77 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: 5.28 Conformation dependent library (CDL) restraints added in 1.4 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: 4.58 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: 3.40 Time building geometry restraints manager: 4.88 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 3.480 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- 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 : 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 % 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 *********************** 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 : 0.697 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.5751 time to fit residues: 151.9668 Evaluate side-chains 66 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8872 ------------------------------------------------------------------------------- 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: 0.1259 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= 0.221 Angle : 0.596 6.019 12639 Z= 0.328 Chirality : 0.042 0.193 1493 Planarity : 0.005 0.043 1027 Dihedral : 17.580 178.339 2512 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.05 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: -0.97 (0.32), residues: 599 helix: 0.26 (0.29), residues: 291 sheet: -0.26 (0.43), residues: 123 loop : -2.29 (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 79 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.672 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 73 average time/residue: 1.3323 time to fit residues: 103.1807 Evaluate side-chains 65 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2131 time to fit residues: 1.1723 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 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: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.1330 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 : 0.757 9.212 12639 Z= 0.406 Chirality : 0.050 0.228 1493 Planarity : 0.006 0.049 1027 Dihedral : 17.884 178.468 2512 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 2.82 % Allowed : 11.47 % Favored : 85.71 % 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: 0.71 (0.30), residues: 285 sheet: -0.18 (0.42), residues: 124 loop : -2.23 (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 86 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.788 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 1.4106 time to fit residues: 119.5040 Evaluate side-chains 76 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4647 time to fit residues: 2.4683 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 87 ASN A 194 HIS B 26 GLN B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8814 Z= 0.170 Angle : 0.543 6.283 12639 Z= 0.297 Chirality : 0.039 0.174 1493 Planarity : 0.004 0.043 1027 Dihedral : 17.461 179.095 2512 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 13.16 % Favored : 84.77 % 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: 0.06 (0.34), residues: 599 helix: 1.26 (0.31), residues: 292 sheet: -0.07 (0.41), residues: 130 loop : -1.92 (0.43), 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 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.750 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 1.3925 time to fit residues: 116.3921 Evaluate side-chains 69 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.8234 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 131 ASN B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8814 Z= 0.200 Angle : 0.555 6.033 12639 Z= 0.302 Chirality : 0.039 0.180 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.449 178.507 2512 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.69 % Allowed : 14.10 % Favored : 84.21 % 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: 0.45 (0.34), residues: 599 helix: 1.60 (0.31), residues: 287 sheet: 0.15 (0.42), residues: 131 loop : -1.71 (0.44), residues: 181 *********************** 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 76 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.793 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 1.4706 time to fit residues: 111.9294 Evaluate side-chains 70 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.0796 time to fit residues: 2.0266 ------------------------------------------------------------------------------- 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: 0.6980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 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 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1722 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= 0.250 Angle : 0.585 6.042 12639 Z= 0.317 Chirality : 0.041 0.194 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.479 178.254 2512 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.72 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: 0.50 (0.35), residues: 599 helix: 1.61 (0.31), residues: 287 sheet: 0.23 (0.43), residues: 131 loop : -1.67 (0.44), residues: 181 *********************** 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 83 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.706 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 1.4497 time to fit residues: 117.9461 Evaluate side-chains 77 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 1.1356 time to fit residues: 4.5459 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3320 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.1794 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= 0.222 Angle : 0.566 6.110 12639 Z= 0.308 Chirality : 0.040 0.189 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.415 178.638 2512 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % 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: 0.60 (0.35), residues: 599 helix: 1.73 (0.31), residues: 286 sheet: 0.24 (0.42), residues: 131 loop : -1.65 (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 74 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.681 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 1.4470 time to fit residues: 108.6012 Evaluate side-chains 73 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6171 time to fit residues: 2.2999 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.0170 chunk 14 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- 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: 0.7859 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 : 0.004 0.035 8814 Z= 0.216 Angle : 0.562 6.094 12639 Z= 0.305 Chirality : 0.040 0.187 1493 Planarity : 0.004 0.041 1027 Dihedral : 17.376 178.538 2512 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.44 % Allowed : 15.04 % Favored : 82.52 % 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: 0.65 (0.35), residues: 599 helix: 1.77 (0.31), residues: 286 sheet: 0.25 (0.42), residues: 131 loop : -1.62 (0.44), residues: 182 *********************** 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 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.739 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 1.3685 time to fit residues: 115.8574 Evaluate side-chains 71 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.8096 ------------------------------------------------------------------------------- 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: 6.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8814 Z= 0.342 Angle : 0.649 7.152 12639 Z= 0.349 Chirality : 0.045 0.210 1493 Planarity : 0.004 0.043 1027 Dihedral : 17.582 178.421 2512 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.69 % Allowed : 16.17 % Favored : 82.14 % 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: 0.41 (0.34), residues: 599 helix: 1.55 (0.31), residues: 285 sheet: 0.33 (0.43), residues: 124 loop : -1.76 (0.42), residues: 190 *********************** 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 75 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.711 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 1.4953 time to fit residues: 113.8906 Evaluate side-chains 72 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.9104 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.1891 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= 0.199 Angle : 0.553 6.566 12639 Z= 0.301 Chirality : 0.039 0.182 1493 Planarity : 0.004 0.042 1027 Dihedral : 17.366 178.942 2512 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.32 % Allowed : 17.11 % Favored : 81.58 % 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: 0.67 (0.35), residues: 599 helix: 1.72 (0.31), residues: 287 sheet: 0.28 (0.42), residues: 131 loop : -1.55 (0.45), residues: 181 ********************** 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: 7 poor density : 64 time to evaluate : 0.703 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 1.4145 time to fit residues: 105.0005 Evaluate side-chains 67 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.8074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1268 > 50: distance: 43 - 46: 7.096 distance: 44 - 48: 6.185 distance: 45 - 68: 7.185 distance: 46 - 47: 4.843 distance: 48 - 49: 10.133 distance: 49 - 50: 5.622 distance: 49 - 52: 3.010 distance: 50 - 51: 7.845 distance: 50 - 56: 10.587 distance: 51 - 77: 27.100 distance: 52 - 53: 9.416 distance: 53 - 54: 3.278 distance: 53 - 55: 11.200 distance: 56 - 57: 10.293 distance: 56 - 62: 6.293 distance: 57 - 58: 3.104 distance: 57 - 60: 9.322 distance: 58 - 63: 12.234 distance: 60 - 61: 9.096 distance: 61 - 62: 11.877 distance: 63 - 64: 5.266 distance: 64 - 65: 7.005 distance: 64 - 67: 4.880 distance: 65 - 66: 19.019 distance: 65 - 68: 4.914 distance: 68 - 69: 6.205 distance: 69 - 70: 7.312 distance: 69 - 72: 9.952 distance: 70 - 71: 36.599 distance: 70 - 77: 13.667 distance: 72 - 73: 5.292 distance: 73 - 74: 8.905 distance: 74 - 75: 12.038 distance: 75 - 76: 8.114 distance: 77 - 78: 19.299 distance: 78 - 79: 13.791 distance: 78 - 81: 9.259 distance: 79 - 80: 37.779 distance: 79 - 86: 17.445 distance: 81 - 82: 14.782 distance: 82 - 83: 17.913 distance: 83 - 84: 17.226 distance: 83 - 85: 15.982 distance: 86 - 87: 15.521 distance: 87 - 88: 10.684 distance: 87 - 90: 25.515 distance: 88 - 89: 3.950 distance: 88 - 95: 7.536 distance: 90 - 91: 16.102 distance: 91 - 92: 12.410 distance: 92 - 93: 16.971 distance: 92 - 94: 37.293 distance: 95 - 96: 7.308 distance: 96 - 97: 13.365 distance: 96 - 99: 20.770 distance: 97 - 98: 3.976 distance: 97 - 103: 7.096 distance: 99 - 100: 22.866 distance: 100 - 101: 34.824 distance: 101 - 102: 35.496 distance: 103 - 104: 13.528 distance: 104 - 105: 12.028 distance: 104 - 107: 9.286 distance: 105 - 106: 6.418 distance: 105 - 111: 10.328 distance: 107 - 108: 11.124 distance: 108 - 109: 13.406 distance: 108 - 110: 12.169 distance: 111 - 112: 17.841 distance: 112 - 113: 16.874 distance: 112 - 115: 15.955 distance: 113 - 114: 21.268 distance: 113 - 118: 15.293 distance: 115 - 116: 28.031 distance: 115 - 117: 19.248