Starting phenix.real_space_refine on Tue Feb 13 18:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i88_35241/02_2024/8i88_35241.pdb" } resolution = 3.7 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= 0.003 sd= 1.000 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 2 5.49 5 S 23 5.16 5 C 4714 2.51 5 N 1210 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 301": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7287 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "B" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3731 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3511 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 408} Time building chain proxies: 4.47, per 1000 atoms: 0.61 Number of scatterers: 7287 At special positions: 0 Unit cell: (78.2, 93.5, 125.8, 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 23 16.00 P 2 15.00 O 1338 8.00 N 1210 7.00 C 4714 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.537A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.081A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.733A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.780A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.676A pdb=" N GLY B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.990A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.164A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.058A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'C' and resid 14 through 29 removed outlier: 3.608A pdb=" N THR C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.675A pdb=" N ASN C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 70' Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.259A pdb=" N ARG C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.155A pdb=" N SER C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.520A pdb=" N GLU C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.533A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 279 Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 353 through 366 Processing helix chain 'C' and resid 369 through 384 removed outlier: 3.593A pdb=" N LEU C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.464A pdb=" N LYS B 2 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.599A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.685A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 319 removed outlier: 7.136A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 419 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 5.988A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.462A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'C' and resid 207 through 210 removed outlier: 3.514A pdb=" N LEU C 214 " --> pdb=" O HIS C 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB3, first strand: chain 'C' and resid 390 through 394 300 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2276 1.34 - 1.46: 1811 1.46 - 1.58: 3349 1.58 - 1.70: 4 1.70 - 1.81: 35 Bond restraints: 7475 Sorted by residual: bond pdb=" CB PRO C 182 " pdb=" CG PRO C 182 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" CG PRO C 182 " pdb=" CD PRO C 182 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 2.01e+00 bond pdb=" CA ASP C 100 " pdb=" CB ASP C 100 " ideal model delta sigma weight residual 1.534 1.557 -0.023 1.76e-02 3.23e+03 1.77e+00 bond pdb=" C PHE C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" CB ASP C 107 " pdb=" CG ASP C 107 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 99.98 - 108.37: 344 108.37 - 116.76: 4831 116.76 - 125.14: 4785 125.14 - 133.53: 126 133.53 - 141.92: 21 Bond angle restraints: 10107 Sorted by residual: angle pdb=" C PRO C 331 " pdb=" N PHE C 332 " pdb=" CA PHE C 332 " ideal model delta sigma weight residual 121.80 141.92 -20.12 2.44e+00 1.68e-01 6.80e+01 angle pdb=" C LYS C 315 " pdb=" CA LYS C 315 " pdb=" CB LYS C 315 " ideal model delta sigma weight residual 117.23 110.21 7.02 1.36e+00 5.41e-01 2.66e+01 angle pdb=" CA PRO C 182 " pdb=" N PRO C 182 " pdb=" CD PRO C 182 " ideal model delta sigma weight residual 112.00 105.21 6.79 1.40e+00 5.10e-01 2.35e+01 angle pdb=" CA LYS C 315 " pdb=" C LYS C 315 " pdb=" N ASP C 316 " ideal model delta sigma weight residual 119.98 116.99 2.99 8.50e-01 1.38e+00 1.24e+01 angle pdb=" N LEU C 37 " pdb=" CA LEU C 37 " pdb=" C LEU C 37 " ideal model delta sigma weight residual 114.75 110.45 4.30 1.26e+00 6.30e-01 1.17e+01 ... (remaining 10102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 3773 16.65 - 33.31: 513 33.31 - 49.96: 149 49.96 - 66.61: 29 66.61 - 83.26: 7 Dihedral angle restraints: 4471 sinusoidal: 1868 harmonic: 2603 Sorted by residual: dihedral pdb=" CA TYR C 330 " pdb=" C TYR C 330 " pdb=" N PRO C 331 " pdb=" CA PRO C 331 " ideal model delta harmonic sigma weight residual 180.00 121.04 58.96 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA ASN C 191 " pdb=" C ASN C 191 " pdb=" N TRP C 192 " pdb=" CA TRP C 192 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET C 193 " pdb=" C MET C 193 " pdb=" N LEU C 194 " pdb=" CA LEU C 194 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 742 0.035 - 0.070: 239 0.070 - 0.105: 67 0.105 - 0.140: 34 0.140 - 0.175: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 60 " pdb=" CA ILE B 60 " pdb=" CG1 ILE B 60 " pdb=" CG2 ILE B 60 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CG LEU B 214 " pdb=" CB LEU B 214 " pdb=" CD1 LEU B 214 " pdb=" CD2 LEU B 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1083 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 181 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO C 182 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 330 " -0.059 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 331 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 331 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 331 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 241 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO C 242 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 242 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 242 " 0.047 5.00e-02 4.00e+02 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 81 2.64 - 3.21: 6343 3.21 - 3.77: 10772 3.77 - 4.34: 14363 4.34 - 4.90: 24114 Nonbonded interactions: 55673 Sorted by model distance: nonbonded pdb=" O PRO C 206 " pdb=" OG1 THR C 216 " model vdw 2.077 2.440 nonbonded pdb=" OG1 THR C 344 " pdb=" O LYS C 349 " model vdw 2.154 2.440 nonbonded pdb=" O VAL C 52 " pdb=" OG1 THR C 57 " model vdw 2.168 2.440 nonbonded pdb=" OD1 ASP C 40 " pdb=" N LYS C 41 " model vdw 2.172 2.520 nonbonded pdb=" OH TYR B 280 " pdb=" OD1 ASP B 458 " model vdw 2.214 2.440 ... (remaining 55668 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 group one per residue 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: 0.360 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: 2.010 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.390 Find NCS groups from input model: 0.210 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:3.100 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 0.087 7475 Z= 0.185 Angle : 0.656 20.119 10107 Z= 0.353 Chirality : 0.042 0.175 1086 Planarity : 0.006 0.115 1268 Dihedral : 16.500 83.263 2789 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 0.38 % Allowed : 23.01 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.14 (0.29), residues: 877 helix: 1.64 (0.32), residues: 277 sheet: 0.64 (0.43), residues: 157 loop : -1.17 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 20 HIS 0.006 0.001 HIS C 160 PHE 0.011 0.001 PHE C 391 TYR 0.014 0.001 TYR B 37 ARG 0.006 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.875 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.1741 time to fit residues: 27.2647 Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7475 Z= 0.188 Angle : 0.538 10.072 10107 Z= 0.277 Chirality : 0.041 0.133 1086 Planarity : 0.005 0.082 1268 Dihedral : 6.090 63.748 984 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 2.91 % Allowed : 22.88 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.24 (0.29), residues: 877 helix: 1.69 (0.31), residues: 282 sheet: 0.60 (0.42), residues: 159 loop : -1.07 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 20 HIS 0.007 0.001 HIS C 160 PHE 0.015 0.001 PHE C 45 TYR 0.007 0.001 TYR C 190 ARG 0.002 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 74 MET cc_start: 0.7651 (ppp) cc_final: 0.7427 (ppp) REVERT: C 138 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: C 192 TRP cc_start: 0.6181 (p90) cc_final: 0.5957 (p90) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.1595 time to fit residues: 26.2162 Evaluate side-chains 108 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7475 Z= 0.250 Angle : 0.566 9.716 10107 Z= 0.292 Chirality : 0.042 0.138 1086 Planarity : 0.005 0.075 1268 Dihedral : 5.775 63.751 981 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 5.31 % Allowed : 22.38 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.13 (0.28), residues: 877 helix: 1.60 (0.31), residues: 282 sheet: 0.40 (0.42), residues: 157 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 PHE 0.013 0.001 PHE C 17 TYR 0.010 0.001 TYR C 171 ARG 0.002 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 305 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7372 (mm) REVERT: C 107 ASP cc_start: 0.7596 (t0) cc_final: 0.7337 (t0) REVERT: C 174 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7996 (p0) REVERT: C 225 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6274 (p90) REVERT: C 276 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.5873 (mmm-85) outliers start: 42 outliers final: 30 residues processed: 132 average time/residue: 0.1643 time to fit residues: 30.3389 Evaluate side-chains 131 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7475 Z= 0.249 Angle : 0.559 9.863 10107 Z= 0.289 Chirality : 0.042 0.131 1086 Planarity : 0.005 0.077 1268 Dihedral : 5.757 63.749 981 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 5.56 % Allowed : 24.27 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.09 (0.28), residues: 877 helix: 1.57 (0.31), residues: 282 sheet: 0.31 (0.42), residues: 157 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 192 HIS 0.005 0.001 HIS C 160 PHE 0.012 0.001 PHE C 60 TYR 0.008 0.001 TYR C 171 ARG 0.002 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 104 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7573 (t0) cc_final: 0.7271 (t0) REVERT: C 174 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (p0) REVERT: C 192 TRP cc_start: 0.6161 (p90) cc_final: 0.5610 (p90) REVERT: C 225 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6391 (p90) REVERT: C 276 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.5837 (mmm-85) outliers start: 44 outliers final: 35 residues processed: 134 average time/residue: 0.1735 time to fit residues: 32.5078 Evaluate side-chains 137 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7475 Z= 0.335 Angle : 0.621 9.417 10107 Z= 0.320 Chirality : 0.044 0.136 1086 Planarity : 0.005 0.077 1268 Dihedral : 6.015 63.757 981 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 6.57 % Allowed : 23.77 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.08 (0.28), residues: 877 helix: 1.39 (0.31), residues: 282 sheet: 0.23 (0.43), residues: 149 loop : -1.13 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 PHE 0.015 0.002 PHE C 17 TYR 0.010 0.001 TYR C 171 ARG 0.002 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 99 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7748 (t0) cc_final: 0.7252 (t0) REVERT: C 174 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8129 (p0) REVERT: C 225 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6429 (p90) REVERT: C 276 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.5872 (mmm-85) outliers start: 52 outliers final: 42 residues processed: 137 average time/residue: 0.1623 time to fit residues: 31.3358 Evaluate side-chains 142 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 97 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7475 Z= 0.340 Angle : 0.628 9.915 10107 Z= 0.324 Chirality : 0.044 0.164 1086 Planarity : 0.005 0.076 1268 Dihedral : 6.119 63.756 981 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 6.83 % Allowed : 23.89 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.37 (0.28), residues: 877 helix: 1.10 (0.31), residues: 290 sheet: -0.11 (0.41), residues: 156 loop : -1.24 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 192 HIS 0.004 0.001 HIS C 160 PHE 0.014 0.001 PHE C 17 TYR 0.015 0.001 TYR C 105 ARG 0.002 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 99 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7725 (t0) cc_final: 0.7257 (t0) REVERT: C 174 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8051 (p0) REVERT: C 225 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6520 (p90) REVERT: C 276 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.5946 (mmm-85) REVERT: C 388 ASP cc_start: 0.8629 (m-30) cc_final: 0.8302 (p0) outliers start: 54 outliers final: 45 residues processed: 141 average time/residue: 0.1644 time to fit residues: 33.0136 Evaluate side-chains 144 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7475 Z= 0.219 Angle : 0.586 10.117 10107 Z= 0.296 Chirality : 0.042 0.173 1086 Planarity : 0.005 0.074 1268 Dihedral : 5.864 63.744 981 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 5.44 % Allowed : 26.17 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.17 (0.29), residues: 877 helix: 1.31 (0.31), residues: 291 sheet: -0.09 (0.41), residues: 163 loop : -1.14 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 20 HIS 0.002 0.001 HIS B 59 PHE 0.011 0.001 PHE C 332 TYR 0.012 0.001 TYR C 105 ARG 0.002 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7669 (t0) cc_final: 0.7236 (t0) REVERT: C 174 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7986 (p0) REVERT: C 225 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6463 (p90) REVERT: C 276 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.5902 (mmm-85) REVERT: C 388 ASP cc_start: 0.8649 (m-30) cc_final: 0.8325 (p0) outliers start: 43 outliers final: 34 residues processed: 142 average time/residue: 0.1592 time to fit residues: 32.0295 Evaluate side-chains 136 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7475 Z= 0.407 Angle : 0.690 9.992 10107 Z= 0.356 Chirality : 0.045 0.180 1086 Planarity : 0.005 0.075 1268 Dihedral : 6.310 63.762 981 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 6.83 % Allowed : 25.28 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.48 (0.28), residues: 877 helix: 1.01 (0.31), residues: 289 sheet: -0.32 (0.41), residues: 157 loop : -1.24 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP C 20 HIS 0.005 0.001 HIS B 59 PHE 0.017 0.002 PHE C 17 TYR 0.013 0.002 TYR B 262 ARG 0.003 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 102 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7785 (t0) cc_final: 0.7383 (t0) REVERT: C 174 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8237 (p0) REVERT: C 225 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6542 (p90) REVERT: C 388 ASP cc_start: 0.8689 (m-30) cc_final: 0.8344 (p0) outliers start: 54 outliers final: 44 residues processed: 145 average time/residue: 0.1671 time to fit residues: 34.4482 Evaluate side-chains 144 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 389 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.176 Angle : 0.604 10.691 10107 Z= 0.303 Chirality : 0.042 0.170 1086 Planarity : 0.005 0.073 1268 Dihedral : 5.793 63.734 981 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 4.42 % Allowed : 27.69 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.11 (0.28), residues: 877 helix: 1.51 (0.31), residues: 288 sheet: -0.10 (0.41), residues: 162 loop : -1.18 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 20 HIS 0.006 0.001 HIS C 226 PHE 0.013 0.001 PHE C 332 TYR 0.017 0.001 TYR B 37 ARG 0.001 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7655 (t0) cc_final: 0.7198 (t0) REVERT: C 174 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7827 (p0) REVERT: C 216 THR cc_start: 0.8098 (m) cc_final: 0.7719 (p) REVERT: C 225 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6427 (p90) REVERT: C 276 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.5990 (mmm-85) REVERT: C 318 ASN cc_start: 0.6288 (m-40) cc_final: 0.5974 (m-40) REVERT: C 388 ASP cc_start: 0.8660 (m-30) cc_final: 0.8359 (p0) outliers start: 35 outliers final: 25 residues processed: 128 average time/residue: 0.1681 time to fit residues: 30.4652 Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7475 Z= 0.319 Angle : 0.659 10.198 10107 Z= 0.336 Chirality : 0.044 0.180 1086 Planarity : 0.005 0.074 1268 Dihedral : 6.093 63.754 981 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 4.55 % Allowed : 28.19 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.29 (0.28), residues: 877 helix: 1.21 (0.31), residues: 294 sheet: -0.22 (0.41), residues: 162 loop : -1.20 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP C 20 HIS 0.003 0.001 HIS B 59 PHE 0.016 0.001 PHE C 332 TYR 0.015 0.001 TYR B 37 ARG 0.003 0.000 ARG B 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7687 (t0) cc_final: 0.7257 (t0) REVERT: C 174 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8082 (p0) REVERT: C 225 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6443 (p90) REVERT: C 276 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8269 (tpt-90) REVERT: C 318 ASN cc_start: 0.6343 (m-40) cc_final: 0.6024 (m-40) REVERT: C 388 ASP cc_start: 0.8681 (m-30) cc_final: 0.8343 (p0) outliers start: 36 outliers final: 31 residues processed: 129 average time/residue: 0.1632 time to fit residues: 29.5875 Evaluate side-chains 131 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132748 restraints weight = 9688.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129235 restraints weight = 9745.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131274 restraints weight = 9765.674| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7475 Z= 0.368 Angle : 0.688 10.536 10107 Z= 0.353 Chirality : 0.045 0.183 1086 Planarity : 0.005 0.074 1268 Dihedral : 6.253 63.756 981 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 5.44 % Allowed : 27.56 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.12 % 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: -0.47 (0.28), residues: 877 helix: 1.02 (0.31), residues: 294 sheet: -0.37 (0.41), residues: 162 loop : -1.25 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C 20 HIS 0.004 0.001 HIS B 59 PHE 0.016 0.002 PHE C 332 TYR 0.014 0.002 TYR B 37 ARG 0.002 0.000 ARG B 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.35 seconds wall clock time: 28 minutes 56.15 seconds (1736.15 seconds total)