Starting phenix.real_space_refine on Mon Nov 18 11:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/11_2024/8psq_17860.cif" } resolution = 2.65 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= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 28 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 5032 2.51 5 N 1457 2.21 5 O 1618 1.98 5 H 7898 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16079 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5030 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 18, 'TRANS': 296} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2221 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "V" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 386 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 466 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 961 SG CYS A 161 48.028 44.792 80.976 1.00 33.76 S ATOM 2850 SG CYS A 282 46.959 47.528 83.512 1.00 39.94 S Time building chain proxies: 9.25, per 1000 atoms: 0.58 Number of scatterers: 16079 At special positions: 0 Unit cell: (88.2, 94.08, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 44 16.00 P 28 15.00 Mg 1 11.99 O 1618 8.00 N 1457 7.00 C 5032 6.00 H 7898 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " Number of angles added : 2 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 47.6% alpha, 13.0% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 8.25 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.510A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.542A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.923A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.770A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.500A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.678A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.658A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.953A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.019A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 498 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.630A pdb=" N LYS C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.700A pdb=" N THR C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.683A pdb=" N SER C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.617A pdb=" N ASP C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 109 removed outlier: 4.148A pdb=" N GLN C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.308A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.308A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.742A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA8, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 83 removed outlier: 9.309A pdb=" N LYS C 73 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N SER C 121 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7876 1.03 - 1.23: 39 1.23 - 1.42: 3518 1.42 - 1.62: 4795 1.62 - 1.81: 64 Bond restraints: 16292 Sorted by residual: bond pdb=" CG1 ILE B 292 " pdb=" CD1 ILE B 292 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.65e-01 bond pdb=" CG PRO A 302 " pdb=" CD PRO A 302 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.33e-01 bond pdb=" CB ASN B 330 " pdb=" CG ASN B 330 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.16e-01 bond pdb=" CB VAL B 357 " pdb=" CG2 VAL B 357 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.15e-01 bond pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta sigma weight residual 1.464 1.455 0.009 1.36e-02 5.41e+03 4.11e-01 ... (remaining 16287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 26442 0.87 - 1.74: 2725 1.74 - 2.62: 176 2.62 - 3.49: 64 3.49 - 4.36: 15 Bond angle restraints: 29422 Sorted by residual: angle pdb=" CA VAL B 324 " pdb=" C VAL B 324 " pdb=" N ALA B 325 " ideal model delta sigma weight residual 116.60 119.58 -2.98 1.45e+00 4.76e-01 4.21e+00 angle pdb=" CG LYS C 36 " pdb=" CD LYS C 36 " pdb=" CE LYS C 36 " ideal model delta sigma weight residual 111.30 115.66 -4.36 2.30e+00 1.89e-01 3.59e+00 angle pdb=" N VAL B 324 " pdb=" CA VAL B 324 " pdb=" C VAL B 324 " ideal model delta sigma weight residual 109.34 113.09 -3.75 2.08e+00 2.31e-01 3.25e+00 angle pdb=" CA ARG C 111 " pdb=" CB ARG C 111 " pdb=" CG ARG C 111 " ideal model delta sigma weight residual 114.10 117.34 -3.24 2.00e+00 2.50e-01 2.63e+00 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 115.66 113.15 2.51 1.63e+00 3.76e-01 2.37e+00 ... (remaining 29417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6722 17.67 - 35.34: 621 35.34 - 53.01: 250 53.01 - 70.68: 68 70.68 - 88.36: 23 Dihedral angle restraints: 7684 sinusoidal: 4444 harmonic: 3240 Sorted by residual: dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP B 337 " pdb=" CB ASP B 337 " pdb=" CG ASP B 337 " pdb=" OD1 ASP B 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG B 33 " pdb=" CD ARG B 33 " pdb=" NE ARG B 33 " pdb=" CZ ARG B 33 " ideal model delta sinusoidal sigma weight residual 90.00 44.80 45.20 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 7681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 885 0.028 - 0.057: 312 0.057 - 0.085: 64 0.085 - 0.113: 47 0.113 - 0.141: 14 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1319 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 470 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 33 " -0.155 9.50e-02 1.11e+02 5.20e-02 3.47e+00 pdb=" NE ARG B 33 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 33 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 33 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 33 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 33 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 33 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 33 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 501 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 502 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " 0.023 5.00e-02 4.00e+02 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1193 2.20 - 2.80: 32246 2.80 - 3.40: 44404 3.40 - 4.00: 60948 4.00 - 4.60: 92406 Nonbonded interactions: 231197 Sorted by model distance: nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.601 2.450 nonbonded pdb=" O2 C V 13 " pdb=" H21 G S 3 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU B 72 " pdb=" H GLU B 72 " model vdw 1.621 2.450 nonbonded pdb=" N3 C V 13 " pdb=" H1 G S 3 " model vdw 1.629 2.600 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.641 2.450 ... (remaining 231192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.280 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 50.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 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 0.029 8394 Z= 0.177 Angle : 0.471 4.359 11475 Z= 0.252 Chirality : 0.035 0.141 1322 Planarity : 0.004 0.069 1372 Dihedral : 18.195 88.356 3322 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.92 % Rotamer: Outliers : 1.19 % Allowed : 22.43 % Favored : 76.37 % 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: 1.30 (0.28), residues: 963 helix: 1.88 (0.26), residues: 437 sheet: -0.06 (0.47), residues: 101 loop : 0.11 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.016 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.012 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.319 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 3.3180 time to fit residues: 443.1905 Evaluate side-chains 123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 444 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8394 Z= 0.176 Angle : 0.468 4.408 11475 Z= 0.248 Chirality : 0.036 0.153 1322 Planarity : 0.004 0.044 1372 Dihedral : 12.253 73.282 1488 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.51 % Allowed : 20.41 % Favored : 77.09 % 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: 1.60 (0.28), residues: 963 helix: 2.13 (0.26), residues: 435 sheet: 0.04 (0.48), residues: 97 loop : 0.29 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.006 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.333 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 132 average time/residue: 3.3800 time to fit residues: 468.5365 Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8394 Z= 0.191 Angle : 0.469 4.391 11475 Z= 0.248 Chirality : 0.036 0.147 1322 Planarity : 0.004 0.057 1372 Dihedral : 12.078 73.324 1479 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.67 % Allowed : 21.24 % Favored : 77.09 % 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: 1.59 (0.27), residues: 963 helix: 2.13 (0.26), residues: 434 sheet: 0.17 (0.49), residues: 95 loop : 0.24 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.016 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7326 (t70) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 3.4254 time to fit residues: 449.0799 Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8394 Z= 0.134 Angle : 0.438 4.279 11475 Z= 0.230 Chirality : 0.035 0.143 1322 Planarity : 0.004 0.061 1372 Dihedral : 11.958 73.359 1479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.91 % Allowed : 20.29 % Favored : 77.80 % 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: 1.73 (0.28), residues: 963 helix: 2.29 (0.26), residues: 435 sheet: 0.22 (0.49), residues: 95 loop : 0.26 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.011 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.008 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7926 (mmp80) cc_final: 0.7195 (mmm160) REVERT: B 103 THR cc_start: 0.9231 (m) cc_final: 0.8742 (p) REVERT: B 155 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: C 93 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7283 (t70) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 3.4338 time to fit residues: 455.0396 Evaluate side-chains 123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8394 Z= 0.269 Angle : 0.507 4.462 11475 Z= 0.270 Chirality : 0.038 0.145 1322 Planarity : 0.004 0.043 1372 Dihedral : 12.189 73.242 1479 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.39 % Allowed : 20.41 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 963 helix: 2.02 (0.25), residues: 434 sheet: 0.27 (0.57), residues: 73 loop : 0.09 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 426 HIS 0.005 0.001 HIS A 367 PHE 0.023 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8528 (t70) cc_final: 0.8267 (t70) REVERT: A 189 ARG cc_start: 0.7997 (mmp80) cc_final: 0.7649 (mmt-90) REVERT: A 323 ASP cc_start: 0.8399 (p0) cc_final: 0.8125 (p0) REVERT: A 332 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8125 (ttp80) REVERT: C 93 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7315 (t70) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 3.3392 time to fit residues: 452.3410 Evaluate side-chains 124 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8394 Z= 0.330 Angle : 0.544 4.570 11475 Z= 0.290 Chirality : 0.039 0.149 1322 Planarity : 0.005 0.039 1372 Dihedral : 12.387 73.303 1479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.46 % Allowed : 20.41 % Favored : 76.13 % 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: 1.16 (0.27), residues: 963 helix: 1.76 (0.25), residues: 434 sheet: 0.30 (0.58), residues: 73 loop : -0.06 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 426 HIS 0.005 0.001 HIS A 367 PHE 0.025 0.002 PHE C 44 TYR 0.015 0.002 TYR A 403 ARG 0.005 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8968 (ttmt) REVERT: A 189 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7688 (mmt-90) REVERT: A 265 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7026 (mtm-85) REVERT: C 93 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7307 (t70) outliers start: 29 outliers final: 15 residues processed: 129 average time/residue: 3.3490 time to fit residues: 453.5179 Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8394 Z= 0.147 Angle : 0.464 4.371 11475 Z= 0.244 Chirality : 0.036 0.144 1322 Planarity : 0.004 0.034 1372 Dihedral : 12.192 73.346 1479 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 21.96 % Favored : 76.37 % 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: 1.45 (0.27), residues: 963 helix: 2.10 (0.25), residues: 434 sheet: -0.01 (0.57), residues: 77 loop : 0.08 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 136 HIS 0.005 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8041 (mmp80) cc_final: 0.7620 (mmt-90) REVERT: B 103 THR cc_start: 0.9248 (m) cc_final: 0.8768 (p) REVERT: C 93 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7285 (t70) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 3.4115 time to fit residues: 420.3736 Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8394 Z= 0.222 Angle : 0.496 4.405 11475 Z= 0.262 Chirality : 0.037 0.144 1322 Planarity : 0.004 0.033 1372 Dihedral : 12.192 73.319 1479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.91 % Allowed : 21.60 % Favored : 76.49 % 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: 1.39 (0.27), residues: 963 helix: 2.02 (0.25), residues: 434 sheet: 0.32 (0.58), residues: 73 loop : 0.00 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.018 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7623 (mmt-90) REVERT: B 461 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7715 (tpp80) REVERT: C 93 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7259 (t70) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 3.2584 time to fit residues: 418.4570 Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 461 ARG Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8394 Z= 0.170 Angle : 0.473 4.443 11475 Z= 0.248 Chirality : 0.036 0.144 1322 Planarity : 0.004 0.034 1372 Dihedral : 12.063 73.337 1479 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 21.84 % Favored : 76.49 % 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: 1.50 (0.27), residues: 963 helix: 2.16 (0.25), residues: 434 sheet: 0.19 (0.57), residues: 75 loop : 0.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.014 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.005 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8466 (t70) cc_final: 0.8100 (t70) REVERT: A 189 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7594 (mmt-90) REVERT: C 93 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7272 (t70) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 3.3040 time to fit residues: 424.6554 Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8394 Z= 0.220 Angle : 0.497 4.403 11475 Z= 0.263 Chirality : 0.037 0.146 1322 Planarity : 0.004 0.034 1372 Dihedral : 11.944 73.412 1479 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.67 % Allowed : 21.72 % Favored : 76.61 % 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: 1.40 (0.27), residues: 963 helix: 2.06 (0.25), residues: 434 sheet: 0.32 (0.58), residues: 73 loop : -0.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.018 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG C 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7603 (mmt-90) REVERT: A 383 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8043 (ttm110) REVERT: C 93 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7282 (t70) outliers start: 14 outliers final: 11 residues processed: 119 average time/residue: 3.4566 time to fit residues: 431.2379 Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.087895 restraints weight = 24572.239| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.30 r_work: 0.2759 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8394 Z= 0.191 Angle : 0.484 4.378 11475 Z= 0.255 Chirality : 0.036 0.144 1322 Planarity : 0.004 0.039 1372 Dihedral : 11.785 73.438 1479 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.91 % Allowed : 21.48 % Favored : 76.61 % 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: 1.46 (0.27), residues: 963 helix: 2.13 (0.25), residues: 434 sheet: 0.22 (0.58), residues: 75 loop : 0.01 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.014 0.001 TYR C 95 ARG 0.011 0.000 ARG A 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7748.94 seconds wall clock time: 137 minutes 26.08 seconds (8246.08 seconds total)