Starting phenix.real_space_refine on Fri Aug 2 22:25:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/08_2024/8rb7_19027.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 1840 2.51 5 N 508 2.21 5 O 538 1.98 5 H 2948 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "B" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 3.39, per 1000 atoms: 0.58 Number of scatterers: 5848 At special positions: 0 Unit cell: (73.216, 134.784, 50.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 538 8.00 N 508 7.00 C 1840 6.00 H 2948 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: 4.42 Conformation dependent library (CDL) restraints added in 617.0 milliseconds 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 688 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 73.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.553A pdb=" N ARG A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 319 removed outlier: 4.203A pdb=" N GLY A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.625A pdb=" N TRP B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.599A pdb=" N ASN B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.808A pdb=" N LEU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 305 through 319 Processing helix chain 'B' and resid 323 through 336 177 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 818 1.09 - 1.27: 2629 1.27 - 1.45: 737 1.45 - 1.63: 1696 1.63 - 1.82: 22 Bond restraints: 5902 Sorted by residual: bond pdb=" N THR A 189 " pdb=" H THR A 189 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N LYS A 164 " pdb=" H LYS A 164 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NH1 ARG A 166 " pdb="HH12 ARG A 166 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH1 ARG A 278 " pdb="HH12 ARG A 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 PHE A 168 " pdb=" HE1 PHE A 168 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 5897 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.35: 84 104.35 - 112.03: 6584 112.03 - 119.72: 2236 119.72 - 127.41: 1773 127.41 - 135.09: 45 Bond angle restraints: 10722 Sorted by residual: angle pdb=" C ASP A 317 " pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 120.38 127.94 -7.56 1.37e+00 5.33e-01 3.05e+01 angle pdb=" C ASP B 317 " pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta sigma weight residual 120.28 127.60 -7.32 1.34e+00 5.57e-01 2.98e+01 angle pdb=" C SER B 250 " pdb=" N GLN B 251 " pdb=" CA GLN B 251 " ideal model delta sigma weight residual 120.44 127.48 -7.04 1.30e+00 5.92e-01 2.93e+01 angle pdb=" C SER A 250 " pdb=" N GLN A 251 " pdb=" CA GLN A 251 " ideal model delta sigma weight residual 120.44 127.35 -6.91 1.30e+00 5.92e-01 2.83e+01 angle pdb=" C LYS B 238 " pdb=" N GLN B 239 " pdb=" CA GLN B 239 " ideal model delta sigma weight residual 120.28 127.12 -6.84 1.34e+00 5.57e-01 2.61e+01 ... (remaining 10717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 2475 18.31 - 36.62: 155 36.62 - 54.94: 59 54.94 - 73.25: 40 73.25 - 91.56: 7 Dihedral angle restraints: 2736 sinusoidal: 1546 harmonic: 1190 Sorted by residual: dihedral pdb=" CA PRO B 322 " pdb=" C PRO B 322 " pdb=" N THR B 323 " pdb=" CA THR B 323 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO A 322 " pdb=" C PRO A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLU B 179 " pdb=" C GLU B 179 " pdb=" N PRO B 180 " pdb=" CA PRO B 180 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 2733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 282 0.083 - 0.165: 128 0.165 - 0.247: 20 0.247 - 0.329: 6 0.329 - 0.411: 6 Chirality restraints: 442 Sorted by residual: chirality pdb=" CA GLN B 313 " pdb=" N GLN B 313 " pdb=" C GLN B 313 " pdb=" CB GLN B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLN A 251 " pdb=" N GLN A 251 " pdb=" C GLN A 251 " pdb=" CB GLN A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LYS B 161 " pdb=" N LYS B 161 " pdb=" C LYS B 161 " pdb=" CB LYS B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 439 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 251 " 0.080 2.00e-02 2.50e+03 4.80e-01 3.46e+03 pdb=" CD GLN A 251 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 251 " -0.085 2.00e-02 2.50e+03 pdb=" NE2 GLN A 251 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 251 " 0.824 2.00e-02 2.50e+03 pdb="HE22 GLN A 251 " -0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 313 " 0.301 2.00e-02 2.50e+03 4.16e-01 2.59e+03 pdb=" CD GLN B 313 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN B 313 " -0.290 2.00e-02 2.50e+03 pdb=" NE2 GLN B 313 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 313 " 0.655 2.00e-02 2.50e+03 pdb="HE22 GLN B 313 " -0.658 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 318 " -0.312 2.00e-02 2.50e+03 3.99e-01 2.38e+03 pdb=" CD GLN A 318 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 318 " 0.306 2.00e-02 2.50e+03 pdb=" NE2 GLN A 318 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN A 318 " -0.627 2.00e-02 2.50e+03 pdb="HE22 GLN A 318 " 0.607 2.00e-02 2.50e+03 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 304 2.18 - 2.78: 10349 2.78 - 3.39: 16154 3.39 - 3.99: 19956 3.99 - 4.60: 29203 Nonbonded interactions: 75966 Sorted by model distance: nonbonded pdb="HH11 ARG A 247 " pdb=" OE1 GLN B 292 " model vdw 1.570 2.450 nonbonded pdb=" HG SER A 266 " pdb=" OE1 GLU A 335 " model vdw 1.595 2.450 nonbonded pdb=" OE1 GLU B 245 " pdb=" HG1 THR B 249 " model vdw 1.634 2.450 nonbonded pdb=" HG SER B 229 " pdb=" OE1 GLU B 232 " model vdw 1.637 2.450 nonbonded pdb=" O VAL B 206 " pdb=" HG SER B 209 " model vdw 1.653 2.450 ... (remaining 75961 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.080 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.014 0.117 2954 Z= 0.906 Angle : 1.834 8.004 3992 Z= 1.226 Chirality : 0.099 0.411 442 Planarity : 0.016 0.103 518 Dihedral : 14.959 91.559 1150 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.96 % Allowed : 2.88 % Favored : 96.15 % 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: -1.02 (0.40), residues: 356 helix: -0.79 (0.28), residues: 243 sheet: None (None), residues: 0 loop : 0.03 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.025 TRP A 205 HIS 0.011 0.005 HIS B 219 PHE 0.045 0.014 PHE A 237 TYR 0.142 0.017 TYR B 162 ARG 0.008 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7437 (ttm170) REVERT: A 306 ASN cc_start: 0.6725 (m-40) cc_final: 0.6311 (p0) REVERT: B 291 ASP cc_start: 0.7782 (p0) cc_final: 0.7415 (p0) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.5522 time to fit residues: 94.6568 Evaluate side-chains 104 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2954 Z= 0.234 Angle : 0.644 5.150 3992 Z= 0.345 Chirality : 0.037 0.154 442 Planarity : 0.006 0.043 518 Dihedral : 5.736 22.767 395 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 10.90 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.43), residues: 356 helix: 0.66 (0.31), residues: 248 sheet: None (None), residues: 0 loop : 0.13 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 184 HIS 0.002 0.001 HIS A 219 PHE 0.013 0.002 PHE A 181 TYR 0.011 0.002 TYR B 162 ARG 0.005 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.9083 (tpp) cc_final: 0.8780 (tpt) REVERT: A 235 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 256 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7397 (ttm170) REVERT: A 292 GLN cc_start: 0.8730 (mt0) cc_final: 0.8484 (tp-100) REVERT: B 197 ILE cc_start: 0.7913 (mm) cc_final: 0.7608 (tp) REVERT: B 211 ARG cc_start: 0.7596 (ptt90) cc_final: 0.6321 (mmt-90) REVERT: B 268 TYR cc_start: 0.7931 (t80) cc_final: 0.7493 (t80) REVERT: B 291 ASP cc_start: 0.7775 (p0) cc_final: 0.7398 (p0) REVERT: B 313 GLN cc_start: 0.8051 (tt0) cc_final: 0.7813 (tp-100) outliers start: 6 outliers final: 3 residues processed: 110 average time/residue: 0.3984 time to fit residues: 49.9830 Evaluate side-chains 91 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2954 Z= 0.166 Angle : 0.555 5.207 3992 Z= 0.291 Chirality : 0.036 0.154 442 Planarity : 0.005 0.053 518 Dihedral : 4.975 19.058 394 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 13.78 % Favored : 84.62 % 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 (0.44), residues: 356 helix: 1.14 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.39 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.002 0.001 HIS B 219 PHE 0.011 0.001 PHE A 181 TYR 0.012 0.001 TYR B 254 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.9051 (tpp) cc_final: 0.8664 (tpt) REVERT: A 256 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7317 (ttm170) REVERT: A 263 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7315 (mt-10) REVERT: B 197 ILE cc_start: 0.8029 (mm) cc_final: 0.7697 (tp) REVERT: B 211 ARG cc_start: 0.7497 (ptt90) cc_final: 0.6428 (mmt180) REVERT: B 291 ASP cc_start: 0.7668 (p0) cc_final: 0.7275 (p0) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.3844 time to fit residues: 46.7127 Evaluate side-chains 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2954 Z= 0.198 Angle : 0.548 5.132 3992 Z= 0.289 Chirality : 0.036 0.150 442 Planarity : 0.005 0.044 518 Dihedral : 4.665 18.438 394 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % Favored : 84.62 % 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: 1.51 (0.44), residues: 356 helix: 1.37 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.34 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.002 0.001 HIS B 219 PHE 0.017 0.001 PHE A 181 TYR 0.012 0.002 TYR B 162 ARG 0.007 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.9010 (tpp) cc_final: 0.8607 (tpt) REVERT: A 235 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 256 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7320 (ttm170) REVERT: B 197 ILE cc_start: 0.7992 (mm) cc_final: 0.7654 (tp) REVERT: B 211 ARG cc_start: 0.7787 (ptt90) cc_final: 0.6600 (mmt180) REVERT: B 268 TYR cc_start: 0.7805 (t80) cc_final: 0.7582 (t80) REVERT: B 291 ASP cc_start: 0.7563 (p0) cc_final: 0.7062 (p0) REVERT: B 296 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8357 (mm-30) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.3875 time to fit residues: 44.6297 Evaluate side-chains 93 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 257 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2954 Z= 0.166 Angle : 0.519 4.894 3992 Z= 0.270 Chirality : 0.035 0.147 442 Planarity : 0.005 0.033 518 Dihedral : 4.459 17.888 394 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.96 % Allowed : 14.74 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.45), residues: 356 helix: 1.42 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.38 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.009 0.001 PHE A 181 TYR 0.007 0.001 TYR B 254 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8476 (tt0) cc_final: 0.8128 (tt0) REVERT: A 218 MET cc_start: 0.9005 (tpp) cc_final: 0.8574 (tpt) REVERT: A 256 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7291 (ttm170) REVERT: B 197 ILE cc_start: 0.7973 (mm) cc_final: 0.7640 (tp) REVERT: B 211 ARG cc_start: 0.7876 (ptt90) cc_final: 0.6562 (mmt180) REVERT: B 291 ASP cc_start: 0.7543 (p0) cc_final: 0.7042 (p0) outliers start: 3 outliers final: 2 residues processed: 109 average time/residue: 0.3836 time to fit residues: 48.0262 Evaluate side-chains 92 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2954 Z= 0.226 Angle : 0.561 6.723 3992 Z= 0.291 Chirality : 0.037 0.206 442 Planarity : 0.005 0.046 518 Dihedral : 4.489 18.648 394 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 15.06 % Favored : 83.01 % 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: 1.56 (0.45), residues: 356 helix: 1.43 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.30 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.001 HIS A 219 PHE 0.008 0.001 PHE A 181 TYR 0.012 0.002 TYR B 162 ARG 0.010 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7074 (m-80) cc_final: 0.5913 (m-80) REVERT: A 256 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7247 (ttm170) REVERT: A 263 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7331 (tt0) REVERT: A 264 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8010 (ttpt) REVERT: B 197 ILE cc_start: 0.7931 (mm) cc_final: 0.7639 (tp) REVERT: B 211 ARG cc_start: 0.8010 (ptt90) cc_final: 0.6816 (mmt180) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.3751 time to fit residues: 40.4473 Evaluate side-chains 93 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 257 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2954 Z= 0.156 Angle : 0.513 6.650 3992 Z= 0.263 Chirality : 0.036 0.170 442 Planarity : 0.005 0.029 518 Dihedral : 4.225 17.792 394 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.96 % Allowed : 15.71 % Favored : 83.33 % 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: 1.74 (0.45), residues: 356 helix: 1.58 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.32 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.000 HIS B 219 PHE 0.009 0.001 PHE A 181 TYR 0.008 0.001 TYR B 268 ARG 0.005 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7027 (m-80) cc_final: 0.5922 (m-80) REVERT: A 218 MET cc_start: 0.9013 (tpp) cc_final: 0.8559 (tpt) REVERT: A 235 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8066 (mm-30) REVERT: A 256 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7180 (ttm170) REVERT: A 264 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7949 (ttpt) REVERT: B 162 TYR cc_start: 0.6309 (t80) cc_final: 0.4399 (t80) REVERT: B 211 ARG cc_start: 0.7965 (ptt90) cc_final: 0.6727 (mmt180) outliers start: 3 outliers final: 2 residues processed: 95 average time/residue: 0.4205 time to fit residues: 45.4841 Evaluate side-chains 91 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2954 Z= 0.206 Angle : 0.535 6.379 3992 Z= 0.279 Chirality : 0.036 0.165 442 Planarity : 0.005 0.054 518 Dihedral : 4.222 18.199 394 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.28 % Allowed : 17.31 % Favored : 81.41 % 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: 1.74 (0.45), residues: 356 helix: 1.54 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.42 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.001 HIS A 219 PHE 0.018 0.001 PHE A 181 TYR 0.011 0.001 TYR B 162 ARG 0.007 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7259 (m-80) cc_final: 0.6039 (m-80) REVERT: A 218 MET cc_start: 0.9005 (tpp) cc_final: 0.8507 (tpt) REVERT: A 235 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8195 (mm-30) REVERT: A 256 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7169 (ttm170) REVERT: A 264 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8105 (ttpt) REVERT: B 162 TYR cc_start: 0.6663 (t80) cc_final: 0.4980 (p90) REVERT: B 211 ARG cc_start: 0.8054 (ptt90) cc_final: 0.6872 (mmt180) REVERT: B 283 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6684 (tpp80) outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 0.4112 time to fit residues: 45.2664 Evaluate side-chains 89 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.7462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2954 Z= 0.173 Angle : 0.526 6.745 3992 Z= 0.271 Chirality : 0.036 0.187 442 Planarity : 0.005 0.043 518 Dihedral : 4.092 17.594 394 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 17.31 % Favored : 82.05 % 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: 1.86 (0.45), residues: 356 helix: 1.62 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.48 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.010 0.001 PHE A 181 TYR 0.008 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7213 (m-80) cc_final: 0.6482 (m-80) REVERT: A 218 MET cc_start: 0.9026 (tpp) cc_final: 0.8509 (tpt) REVERT: A 235 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 256 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7171 (ttm170) REVERT: A 264 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8169 (ttpt) REVERT: B 162 TYR cc_start: 0.6632 (t80) cc_final: 0.4857 (p90) REVERT: B 211 ARG cc_start: 0.8049 (ptt90) cc_final: 0.6813 (mmt180) REVERT: B 283 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6773 (tpp80) REVERT: B 292 GLN cc_start: 0.8686 (mt0) cc_final: 0.8344 (tp40) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.4083 time to fit residues: 42.0048 Evaluate side-chains 87 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.7608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2954 Z= 0.166 Angle : 0.538 6.509 3992 Z= 0.278 Chirality : 0.036 0.180 442 Planarity : 0.005 0.043 518 Dihedral : 4.130 17.253 394 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 17.95 % Favored : 81.41 % 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: 1.91 (0.45), residues: 356 helix: 1.67 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.47 (0.64), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.001 0.000 HIS B 219 PHE 0.009 0.001 PHE A 181 TYR 0.006 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7188 (m-80) cc_final: 0.5889 (m-80) REVERT: A 218 MET cc_start: 0.9013 (tpp) cc_final: 0.8487 (tpt) REVERT: A 235 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 256 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7153 (ttm170) REVERT: A 263 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7421 (tt0) REVERT: B 162 TYR cc_start: 0.6571 (t80) cc_final: 0.4809 (p90) REVERT: B 211 ARG cc_start: 0.8031 (ptt90) cc_final: 0.6805 (mmt180) REVERT: B 283 ARG cc_start: 0.7376 (ttm110) cc_final: 0.6734 (tpp80) REVERT: B 292 GLN cc_start: 0.8708 (mt0) cc_final: 0.8373 (tp40) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.3987 time to fit residues: 41.1167 Evaluate side-chains 88 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147903 restraints weight = 12979.058| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 4.20 r_work: 0.3650 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2954 Z= 0.201 Angle : 0.556 6.188 3992 Z= 0.289 Chirality : 0.036 0.178 442 Planarity : 0.005 0.039 518 Dihedral : 4.107 17.697 394 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.32 % Allowed : 18.59 % Favored : 81.09 % 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: 1.87 (0.45), residues: 356 helix: 1.64 (0.33), residues: 250 sheet: None (None), residues: 0 loop : 0.43 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.017 0.001 PHE A 181 TYR 0.011 0.001 TYR B 162 ARG 0.005 0.001 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.84 seconds wall clock time: 40 minutes 32.78 seconds (2432.78 seconds total)