Starting phenix.real_space_refine on Tue Apr 9 09:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/04_2024/8psq_17860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/04_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_17860/04_2024/8psq_17860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/04_2024/8psq_17860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/04_2024/8psq_17860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psq_17860/04_2024/8psq_17860.pdb" } 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 Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.61, per 1000 atoms: 0.47 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 - 3.50 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: 13.22 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: 7.84 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: 6.63 Time building geometry restraints manager: 13.56 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: 99.24 - 106.20: 335 106.20 - 113.15: 19079 113.15 - 120.10: 5035 120.10 - 127.05: 4831 127.05 - 134.00: 142 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 1.850 nonbonded pdb=" O2 C V 13 " pdb=" H21 G S 3 " model vdw 1.606 1.850 nonbonded pdb=" OE1 GLU B 72 " pdb=" H GLU B 72 " model vdw 1.621 1.850 nonbonded pdb=" N3 C V 13 " pdb=" H1 G S 3 " model vdw 1.629 2.000 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.641 1.850 ... (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 ========== 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: 1.430 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: 0.220 Extract box with map and model: 6.250 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 65.300 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.020 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.348 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 3.2239 time to fit residues: 430.4790 Evaluate side-chains 123 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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: 0.8789 moved from start: 0.0406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8394 Z= 0.204 Angle : 0.470 4.456 11475 Z= 0.248 Chirality : 0.036 0.155 1322 Planarity : 0.004 0.041 1372 Dihedral : 12.211 73.284 1488 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 21.24 % 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 (0.28), residues: 963 helix: 2.06 (0.26), residues: 435 sheet: -0.03 (0.47), residues: 99 loop : 0.23 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 371 PHE 0.017 0.001 PHE C 44 TYR 0.012 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 134 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.208 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 127 average time/residue: 3.2831 time to fit residues: 437.8049 Evaluate side-chains 122 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER 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 290 ASP 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: 1.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8394 Z= 0.291 Angle : 0.517 4.525 11475 Z= 0.276 Chirality : 0.038 0.150 1322 Planarity : 0.005 0.038 1372 Dihedral : 12.302 73.321 1479 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.22 % Allowed : 19.81 % Favored : 76.97 % 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: 1.27 (0.27), residues: 963 helix: 1.80 (0.25), residues: 435 sheet: 0.15 (0.48), residues: 95 loop : 0.10 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 346 HIS 0.005 0.001 HIS A 371 PHE 0.023 0.002 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.001 ARG C 68 *********************** 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 140 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7657 (mmp80) REVERT: A 383 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8191 (ttm110) REVERT: C 93 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7340 (t70) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 3.4029 time to fit residues: 461.6001 Evaluate side-chains 128 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 383 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 281 THR 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 487 ARG 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: 0.9980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8797 moved from start: 0.0781 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= 0.185 Angle : 0.464 4.395 11475 Z= 0.246 Chirality : 0.036 0.146 1322 Planarity : 0.004 0.059 1372 Dihedral : 12.190 73.339 1479 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.39 % Allowed : 20.76 % Favored : 76.85 % 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: 1.97 (0.25), residues: 435 sheet: -0.02 (0.48), residues: 97 loop : 0.16 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.016 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.009 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 137 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7635 (mmp80) REVERT: A 323 ASP cc_start: 0.8301 (p0) cc_final: 0.8080 (p0) REVERT: A 383 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8153 (ttm110) REVERT: B 103 THR cc_start: 0.9246 (m) cc_final: 0.8753 (p) REVERT: C 93 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7301 (t70) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 3.2834 time to fit residues: 444.7616 Evaluate side-chains 129 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 24 ASP 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 281 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 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 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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: 0.8825 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8394 Z= 0.296 Angle : 0.520 4.527 11475 Z= 0.277 Chirality : 0.038 0.147 1322 Planarity : 0.005 0.063 1372 Dihedral : 12.372 73.365 1479 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.22 % Allowed : 20.17 % 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: 1.14 (0.27), residues: 963 helix: 1.72 (0.25), residues: 435 sheet: 0.24 (0.56), residues: 73 loop : -0.04 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.022 0.002 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.009 0.001 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 139 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7704 (mmp80) REVERT: A 255 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8688 (mtt) REVERT: A 383 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8195 (ttm110) REVERT: C 93 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7300 (t70) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 3.3531 time to fit residues: 444.0879 Evaluate side-chains 131 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR 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 281 THR 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 487 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8823 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8394 Z= 0.280 Angle : 0.513 4.527 11475 Z= 0.273 Chirality : 0.038 0.149 1322 Planarity : 0.005 0.068 1372 Dihedral : 12.381 73.505 1478 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.34 % Allowed : 19.93 % Favored : 76.73 % 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: 1.09 (0.27), residues: 963 helix: 1.70 (0.25), residues: 435 sheet: 0.16 (0.56), residues: 73 loop : -0.07 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.021 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.011 0.001 ARG B 33 *********************** 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 137 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8428 (p0) cc_final: 0.8156 (p0) REVERT: B 461 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7762 (tpp80) REVERT: C 93 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7290 (t70) outliers start: 28 outliers final: 16 residues processed: 125 average time/residue: 3.3621 time to fit residues: 441.4789 Evaluate side-chains 127 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 24 ASP 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 281 THR 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 461 ARG 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: 0.0370 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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: 0.8785 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8394 Z= 0.147 Angle : 0.448 4.320 11475 Z= 0.236 Chirality : 0.035 0.144 1322 Planarity : 0.004 0.050 1372 Dihedral : 12.169 73.395 1478 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 21.48 % Favored : 76.85 % 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: -0.07 (0.56), residues: 77 loop : 0.09 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.002 0.001 HIS A 371 PHE 0.012 0.001 PHE C 44 TYR 0.011 0.001 TYR C 95 ARG 0.009 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 131 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8200 (p0) cc_final: 0.7957 (p0) REVERT: B 103 THR cc_start: 0.9239 (m) cc_final: 0.8755 (p) REVERT: C 93 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7273 (t70) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 3.2772 time to fit residues: 430.7185 Evaluate side-chains 126 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 67 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 281 THR 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: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.8812 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8394 Z= 0.244 Angle : 0.497 4.455 11475 Z= 0.263 Chirality : 0.037 0.150 1322 Planarity : 0.005 0.080 1372 Dihedral : 12.122 73.441 1478 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.39 % Allowed : 21.24 % 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: 1.29 (0.27), residues: 963 helix: 1.90 (0.25), residues: 435 sheet: 0.10 (0.56), residues: 75 loop : 0.03 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.019 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.012 0.001 ARG B 33 *********************** 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 130 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8394 (p0) cc_final: 0.8159 (p0) REVERT: B 103 THR cc_start: 0.9252 (m) cc_final: 0.8769 (p) REVERT: B 444 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8995 (p0) REVERT: B 461 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7800 (mpp80) REVERT: C 93 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7287 (t70) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 3.1943 time to fit residues: 410.0729 Evaluate side-chains 123 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 67 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 281 THR 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 81 SER 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: 0.2980 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8810 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8394 Z= 0.229 Angle : 0.491 4.436 11475 Z= 0.260 Chirality : 0.037 0.147 1322 Planarity : 0.004 0.073 1372 Dihedral : 11.913 73.428 1478 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.03 % Allowed : 21.60 % 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: 1.31 (0.27), residues: 963 helix: 1.90 (0.25), residues: 435 sheet: 0.03 (0.48), residues: 95 loop : 0.09 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.016 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.012 0.000 ARG B 33 *********************** 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 125 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8362 (p0) cc_final: 0.8128 (p0) REVERT: A 383 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8103 (ttm110) REVERT: B 103 THR cc_start: 0.9257 (m) cc_final: 0.8768 (p) REVERT: B 461 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7795 (mpp80) REVERT: C 93 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7279 (t70) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 3.3928 time to fit residues: 421.0880 Evaluate side-chains 123 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 67 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 281 THR Chi-restraints excluded: chain B residue 294 SER 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 81 SER 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: 0.8980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1085 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= 0.171 Angle : 0.466 4.347 11475 Z= 0.244 Chirality : 0.036 0.144 1322 Planarity : 0.004 0.068 1372 Dihedral : 11.719 73.410 1476 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 21.84 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 963 helix: 2.08 (0.25), residues: 434 sheet: 0.03 (0.49), residues: 95 loop : 0.15 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 PHE 0.014 0.001 PHE C 44 TYR 0.013 0.001 TYR C 95 ARG 0.011 0.000 ARG B 33 ********************** 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 fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7675 (mtp180) REVERT: A 323 ASP cc_start: 0.8242 (p0) cc_final: 0.8012 (p0) REVERT: A 383 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8089 (ttm110) REVERT: B 103 THR cc_start: 0.9240 (m) cc_final: 0.8756 (p) REVERT: B 461 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7809 (mpp80) REVERT: C 93 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7307 (t70) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 3.5032 time to fit residues: 438.3050 Evaluate side-chains 123 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 67 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 281 THR Chi-restraints excluded: chain B residue 294 SER 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 81 SER 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: 2.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.110944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.087035 restraints weight = 24705.995| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.38 r_work: 0.2747 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 : 0.003 0.029 8394 Z= 0.211 Angle : 0.485 4.400 11475 Z= 0.256 Chirality : 0.037 0.144 1322 Planarity : 0.004 0.066 1372 Dihedral : 11.743 73.363 1476 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 21.00 % Favored : 76.85 % 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: 1.36 (0.27), residues: 963 helix: 1.97 (0.25), residues: 435 sheet: 0.11 (0.56), residues: 75 loop : 0.05 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.016 0.001 PHE C 44 TYR 0.014 0.001 TYR C 95 ARG 0.010 0.000 ARG B 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7729.87 seconds wall clock time: 136 minutes 58.65 seconds (8218.65 seconds total)