Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 23:14:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/07_2023/7yi8_33853_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3334 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.58 Number of scatterers: 5225 At special positions: 0 Unit cell: (70.55, 73.1, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 972 8.00 N 892 7.00 C 3334 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: 1.94 Conformation dependent library (CDL) restraints added in 736.9 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 2 sheets defined 31.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 106 through 109 No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.607A pdb=" N ASN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 255 through 267 removed outlier: 5.361A pdb=" N ARG B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'C' and resid 170 through 182 removed outlier: 4.377A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 removed outlier: 3.603A pdb=" N LYS D 19 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 52 through 64 Processing helix chain 'D' and resid 84 through 95 removed outlier: 4.419A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing sheet with id= A, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.616A pdb=" N ILE A 183 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG A 366 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR A 207 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 176 through 180 removed outlier: 6.709A pdb=" N TRP B 365 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 179 " --> pdb=" O TRP B 365 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 367 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 353 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 205 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 354 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET B 207 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE B 248 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET B 208 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 250 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 306 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU B 272 " --> pdb=" O VAL B 306 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1406 1.33 - 1.45: 870 1.45 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5318 Sorted by residual: bond pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C8 SAH B 401 " pdb=" N7 SAH B 401 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C2 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C6 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1' SAH B 401 " pdb=" N9 SAH B 401 " ideal model delta sigma weight residual 1.440 1.476 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 5313 not shown) Histogram of bond angle deviations from ideal: 91.43 - 99.94: 3 99.94 - 108.46: 211 108.46 - 116.97: 3554 116.97 - 125.49: 3303 125.49 - 134.00: 76 Bond angle restraints: 7147 Sorted by residual: angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 91.43 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O SAH B 401 " pdb=" C SAH B 401 " pdb=" OXT SAH B 401 " ideal model delta sigma weight residual 126.79 117.95 8.84 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C LYS B 317 " pdb=" N ASN B 318 " pdb=" CA ASN B 318 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " pdb=" C4 SAH B 401 " ideal model delta sigma weight residual 111.67 120.13 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N1 SAH B 401 " pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 128.45 120.52 7.93 3.00e+00 1.11e-01 6.99e+00 ... (remaining 7142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 2895 17.61 - 35.23: 266 35.23 - 52.84: 60 52.84 - 70.45: 10 70.45 - 88.07: 6 Dihedral angle restraints: 3237 sinusoidal: 1382 harmonic: 1855 Sorted by residual: dihedral pdb=" CA MET A 401 " pdb=" C MET A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " ideal model delta sinusoidal sigma weight residual -90.00 -134.61 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 201 " pdb=" CG GLU A 201 " pdb=" CD GLU A 201 " pdb=" OE1 GLU A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -88.07 88.07 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 489 0.034 - 0.068: 212 0.068 - 0.102: 50 0.102 - 0.136: 26 0.136 - 0.170: 3 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA GLN B 155 " pdb=" N GLN B 155 " pdb=" C GLN B 155 " pdb=" CB GLN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 777 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 151 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C LEU B 151 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 151 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO A 353 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 51 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 52 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " 0.023 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 203 2.72 - 3.27: 5188 3.27 - 3.81: 8170 3.81 - 4.36: 10546 4.36 - 4.90: 17653 Nonbonded interactions: 41760 Sorted by model distance: nonbonded pdb=" OG SER B 326 " pdb=" OE2 GLU B 337 " model vdw 2.179 2.440 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 261 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 383 " pdb=" NZ LYS B 289 " model vdw 2.257 2.520 nonbonded pdb=" O CYS B 346 " pdb=" OH TYR B 351 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR A 407 " pdb=" OE1 GLU A 431 " model vdw 2.286 2.440 ... (remaining 41755 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.350 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.003 0.059 5318 Z= 0.187 Angle : 0.608 10.344 7147 Z= 0.301 Chirality : 0.043 0.170 780 Planarity : 0.004 0.047 909 Dihedral : 14.732 88.067 2031 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 620 helix: 0.07 (0.37), residues: 193 sheet: -0.33 (0.47), residues: 104 loop : -0.51 (0.36), residues: 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.685 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.1187 time to fit residues: 143.7915 Evaluate side-chains 81 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 5318 Z= 0.312 Angle : 0.632 8.167 7147 Z= 0.326 Chirality : 0.044 0.157 780 Planarity : 0.004 0.056 909 Dihedral : 5.135 44.691 676 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.99 % 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: -0.78 (0.33), residues: 620 helix: -0.36 (0.36), residues: 192 sheet: -0.33 (0.48), residues: 104 loop : -0.58 (0.35), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 99 average time/residue: 1.0697 time to fit residues: 110.9875 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.7734 time to fit residues: 2.5294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.0020 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 380 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5318 Z= 0.163 Angle : 0.514 6.284 7147 Z= 0.268 Chirality : 0.040 0.140 780 Planarity : 0.004 0.049 909 Dihedral : 4.878 52.549 676 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 4.16 % 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: -0.63 (0.33), residues: 620 helix: -0.10 (0.37), residues: 190 sheet: -0.23 (0.47), residues: 105 loop : -0.58 (0.35), residues: 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.635 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 101 average time/residue: 0.9864 time to fit residues: 104.7574 Evaluate side-chains 94 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1118 time to fit residues: 1.3304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 241 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 5318 Z= 0.156 Angle : 0.499 6.234 7147 Z= 0.259 Chirality : 0.040 0.135 780 Planarity : 0.004 0.048 909 Dihedral : 4.715 52.159 676 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 4.68 % 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 (0.33), residues: 620 helix: -0.16 (0.37), residues: 197 sheet: -0.08 (0.49), residues: 105 loop : -0.62 (0.35), residues: 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 0.631 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 100 average time/residue: 0.9863 time to fit residues: 103.8015 Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.6274 time to fit residues: 2.8386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 241 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5318 Z= 0.191 Angle : 0.534 7.284 7147 Z= 0.275 Chirality : 0.041 0.141 780 Planarity : 0.004 0.050 909 Dihedral : 4.733 49.330 676 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.33), residues: 620 helix: -0.21 (0.37), residues: 198 sheet: -0.07 (0.49), residues: 105 loop : -0.67 (0.35), residues: 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.687 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 93 average time/residue: 0.9655 time to fit residues: 94.5709 Evaluate side-chains 91 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.7705 time to fit residues: 4.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 34 optimal weight: 0.0970 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5318 Z= 0.146 Angle : 0.509 6.995 7147 Z= 0.262 Chirality : 0.040 0.150 780 Planarity : 0.004 0.048 909 Dihedral : 4.624 51.692 676 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 620 helix: -0.12 (0.37), residues: 198 sheet: 0.10 (0.50), residues: 104 loop : -0.69 (0.35), residues: 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.663 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.9489 time to fit residues: 94.2487 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0777 time to fit residues: 1.1228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 5318 Z= 0.329 Angle : 0.632 6.968 7147 Z= 0.324 Chirality : 0.043 0.158 780 Planarity : 0.004 0.056 909 Dihedral : 4.981 35.936 676 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 4.68 % 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: -0.98 (0.33), residues: 620 helix: -0.53 (0.35), residues: 198 sheet: -0.19 (0.52), residues: 95 loop : -0.79 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 0.638 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 91 average time/residue: 1.0868 time to fit residues: 104.2078 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.3235 time to fit residues: 3.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 5318 Z= 0.156 Angle : 0.523 7.767 7147 Z= 0.269 Chirality : 0.040 0.167 780 Planarity : 0.004 0.053 909 Dihedral : 4.707 47.357 676 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 2.43 % 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: -0.78 (0.33), residues: 620 helix: -0.26 (0.37), residues: 198 sheet: 0.03 (0.53), residues: 94 loop : -0.77 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.662 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 91 average time/residue: 1.0899 time to fit residues: 104.2009 Evaluate side-chains 85 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 5318 Z= 0.266 Angle : 0.609 7.704 7147 Z= 0.309 Chirality : 0.043 0.174 780 Planarity : 0.004 0.057 909 Dihedral : 4.798 36.354 676 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 2.43 % 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: -0.89 (0.33), residues: 620 helix: -0.41 (0.36), residues: 197 sheet: -0.04 (0.53), residues: 95 loop : -0.80 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.633 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.9307 time to fit residues: 87.3967 Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0472 time to fit residues: 0.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 5318 Z= 0.367 Angle : 0.683 8.098 7147 Z= 0.347 Chirality : 0.045 0.207 780 Planarity : 0.005 0.060 909 Dihedral : 5.163 34.411 676 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.25 % 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: -1.12 (0.32), residues: 620 helix: -0.71 (0.35), residues: 196 sheet: -0.18 (0.53), residues: 95 loop : -0.87 (0.34), residues: 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.633 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.8680 time to fit residues: 79.1110 Evaluate side-chains 82 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1062 time to fit residues: 1.0561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.184816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149498 restraints weight = 6090.730| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.31 r_work: 0.3703 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5318 Z= 0.179 Angle : 0.570 8.361 7147 Z= 0.289 Chirality : 0.041 0.184 780 Planarity : 0.004 0.054 909 Dihedral : 4.827 45.599 676 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 2.43 % 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: -0.94 (0.33), residues: 620 helix: -0.40 (0.36), residues: 197 sheet: -0.04 (0.54), residues: 94 loop : -0.87 (0.34), residues: 329 =============================================================================== Job complete usr+sys time: 2310.00 seconds wall clock time: 41 minutes 36.38 seconds (2496.38 seconds total)