Starting phenix.real_space_refine on Sun Mar 10 22:57:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/03_2024/8rb7_19027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/03_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_19027/03_2024/8rb7_19027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/03_2024/8rb7_19027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/03_2024/8rb7_19027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb7_19027/03_2024/8rb7_19027.pdb" } 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-5265/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: 3.16, per 1000 atoms: 0.54 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: 4.91 Conformation dependent library (CDL) restraints added in 633.6 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: 0.56 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: 1.91 Time building geometry restraints manager: 4.99 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 1.850 nonbonded pdb=" HG SER A 266 " pdb=" OE1 GLU A 335 " model vdw 1.595 1.850 nonbonded pdb=" OE1 GLU B 245 " pdb=" HG1 THR B 249 " model vdw 1.634 1.850 nonbonded pdb=" HG SER B 229 " pdb=" OE1 GLU B 232 " model vdw 1.637 1.850 nonbonded pdb=" O VAL B 206 " pdb=" HG SER B 209 " model vdw 1.653 1.850 ... (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 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: 0.470 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: 0.090 Extract box with map and model: 2.520 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- 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 : 0.483 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: 0.5712 time to fit residues: 97.9620 Evaluate side-chains 104 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7281 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2954 Z= 0.248 Angle : 0.647 5.427 3992 Z= 0.349 Chirality : 0.037 0.154 442 Planarity : 0.006 0.042 518 Dihedral : 5.745 23.123 395 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 11.22 % Favored : 86.22 % 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: 0.73 (0.43), residues: 356 helix: 0.71 (0.31), residues: 248 sheet: None (None), residues: 0 loop : 0.25 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 184 HIS 0.003 0.001 HIS A 219 PHE 0.014 0.002 PHE A 181 TYR 0.013 0.002 TYR B 162 ARG 0.004 0.001 ARG B 204 *********************** 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 116 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.487 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: 0.9089 (tpp) cc_final: 0.8768 (tpt) REVERT: A 256 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7418 (ttm170) REVERT: A 292 GLN cc_start: 0.8801 (mt0) cc_final: 0.8568 (tp40) REVERT: B 211 ARG cc_start: 0.7370 (ptt90) cc_final: 0.6221 (mmt-90) REVERT: B 263 GLU cc_start: 0.7252 (tt0) cc_final: 0.7047 (tt0) REVERT: B 268 TYR cc_start: 0.7925 (t80) cc_final: 0.7684 (t80) REVERT: B 291 ASP cc_start: 0.7755 (p0) cc_final: 0.7318 (p0) REVERT: B 313 GLN cc_start: 0.8092 (tt0) cc_final: 0.7855 (tp-100) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.4926 time to fit residues: 61.9208 Evaluate side-chains 103 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 323 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: 1.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7262 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2954 Z= 0.162 Angle : 0.551 5.275 3992 Z= 0.287 Chirality : 0.035 0.153 442 Planarity : 0.006 0.053 518 Dihedral : 5.043 19.712 394 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.92 % Allowed : 14.10 % Favored : 83.97 % 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: 1.46 (0.44), residues: 356 helix: 1.26 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.52 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.010 0.001 PHE A 181 TYR 0.012 0.001 TYR B 254 ARG 0.007 0.001 ARG B 287 *********************** 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 117 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.480 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 190 GLU cc_start: 0.8498 (tt0) cc_final: 0.8194 (tt0) REVERT: A 218 MET cc_start: 0.9047 (tpp) cc_final: 0.8657 (tpt) REVERT: A 256 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7325 (ttm170) REVERT: A 292 GLN cc_start: 0.8704 (mt0) cc_final: 0.8478 (tp-100) REVERT: B 291 ASP cc_start: 0.7664 (p0) cc_final: 0.7175 (p0) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.3945 time to fit residues: 51.1489 Evaluate side-chains 92 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.7303 moved from start: 0.6374 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= 0.187 Angle : 0.544 5.091 3992 Z= 0.283 Chirality : 0.035 0.148 442 Planarity : 0.005 0.047 518 Dihedral : 4.683 19.308 394 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.92 % Allowed : 15.38 % Favored : 82.69 % 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: 1.62 (0.45), residues: 356 helix: 1.40 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.53 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 309 HIS 0.001 0.001 HIS B 219 PHE 0.015 0.001 PHE A 181 TYR 0.011 0.001 TYR B 162 ARG 0.003 0.000 ARG A 283 *********************** 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 101 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.486 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: A 162 TYR cc_start: 0.6735 (m-80) cc_final: 0.5797 (m-80) REVERT: A 218 MET cc_start: 0.9014 (tpp) cc_final: 0.8596 (tpt) REVERT: A 256 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7300 (ttm170) REVERT: B 259 GLN cc_start: 0.7876 (tt0) cc_final: 0.7626 (tt0) REVERT: B 268 TYR cc_start: 0.7760 (t80) cc_final: 0.7483 (t80) REVERT: B 291 ASP cc_start: 0.7475 (p0) cc_final: 0.6959 (p0) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.4478 time to fit residues: 48.8316 Evaluate side-chains 92 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 323 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: 9.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7343 moved from start: 0.6748 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= 0.212 Angle : 0.549 4.967 3992 Z= 0.287 Chirality : 0.035 0.145 442 Planarity : 0.005 0.036 518 Dihedral : 4.546 18.653 394 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.24 % Allowed : 17.31 % Favored : 80.45 % 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: 1.68 (0.45), residues: 356 helix: 1.43 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.59 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.002 0.001 HIS B 219 PHE 0.014 0.001 PHE A 181 TYR 0.011 0.001 TYR B 162 ARG 0.008 0.001 ARG B 287 *********************** 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 100 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.508 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: A 162 TYR cc_start: 0.6994 (m-80) cc_final: 0.5889 (m-80) REVERT: A 218 MET cc_start: 0.9021 (tpp) cc_final: 0.8600 (tpt) REVERT: A 256 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7304 (ttm170) REVERT: B 259 GLN cc_start: 0.7938 (tt0) cc_final: 0.7726 (tt0) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.4077 time to fit residues: 44.4720 Evaluate side-chains 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 266 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.7327 moved from start: 0.7027 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= 0.167 Angle : 0.498 4.945 3992 Z= 0.260 Chirality : 0.034 0.147 442 Planarity : 0.005 0.028 518 Dihedral : 4.293 18.018 394 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.96 % Allowed : 18.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.45), residues: 356 helix: 1.59 (0.32), residues: 246 sheet: None (None), residues: 0 loop : 0.53 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.011 0.001 PHE A 181 TYR 0.008 0.001 TYR B 162 ARG 0.005 0.000 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 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.406 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: A 162 TYR cc_start: 0.7019 (m-80) cc_final: 0.5958 (m-80) REVERT: A 178 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 256 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7295 (ttm170) REVERT: B 259 GLN cc_start: 0.8125 (tt0) cc_final: 0.7873 (tt0) outliers start: 3 outliers final: 0 residues processed: 94 average time/residue: 0.4097 time to fit residues: 44.1742 Evaluate side-chains 86 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.7340 moved from start: 0.7251 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= 0.176 Angle : 0.516 6.911 3992 Z= 0.263 Chirality : 0.035 0.151 442 Planarity : 0.005 0.027 518 Dihedral : 4.193 17.547 394 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 18.91 % Favored : 79.81 % 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: 1.68 (0.33), residues: 246 sheet: None (None), residues: 0 loop : 0.49 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.006 0.001 PHE B 181 TYR 0.008 0.001 TYR B 162 ARG 0.004 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 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.509 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: 0.7120 (m-80) cc_final: 0.6032 (m-80) REVERT: A 178 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 218 MET cc_start: 0.9012 (tpp) cc_final: 0.8542 (tpt) REVERT: A 256 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7276 (ttm170) REVERT: B 162 TYR cc_start: 0.6417 (t80) cc_final: 0.4422 (t80) REVERT: B 259 GLN cc_start: 0.8094 (tt0) cc_final: 0.7891 (tt0) outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.4317 time to fit residues: 45.6534 Evaluate side-chains 89 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain B residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7313 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2954 Z= 0.150 Angle : 0.497 5.939 3992 Z= 0.252 Chirality : 0.035 0.147 442 Planarity : 0.005 0.039 518 Dihedral : 4.010 16.668 394 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.64 % Allowed : 20.19 % Favored : 79.17 % 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: 2.05 (0.45), residues: 356 helix: 1.76 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.61 (0.66), residues: 108 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 0.008 0.001 PHE A 181 TYR 0.006 0.001 TYR B 162 ARG 0.005 0.000 ARG A 278 *********************** 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 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 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: A 162 TYR cc_start: 0.7110 (m-80) cc_final: 0.6052 (m-80) REVERT: A 256 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7254 (ttm170) REVERT: B 162 TYR cc_start: 0.6350 (t80) cc_final: 0.4395 (t80) REVERT: B 292 GLN cc_start: 0.8619 (mt0) cc_final: 0.8257 (tp40) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.4197 time to fit residues: 45.4784 Evaluate side-chains 90 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 ILE 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: 0.7980 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.7369 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2954 Z= 0.205 Angle : 0.536 5.421 3992 Z= 0.278 Chirality : 0.035 0.138 442 Planarity : 0.005 0.062 518 Dihedral : 4.067 17.215 394 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.64 % Allowed : 21.15 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.45), residues: 356 helix: 1.73 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.54 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.019 0.001 PHE A 181 TYR 0.012 0.001 TYR B 162 ARG 0.012 0.001 ARG B 287 *********************** 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 : 0.563 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: 0.7291 (m-80) cc_final: 0.6096 (m-80) REVERT: A 256 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7233 (ttm170) REVERT: B 162 TYR cc_start: 0.6744 (t80) cc_final: 0.4927 (p90) REVERT: B 211 ARG cc_start: 0.8031 (ptt90) cc_final: 0.6879 (mmt180) REVERT: B 283 ARG cc_start: 0.7273 (ttm110) cc_final: 0.6638 (tpp80) REVERT: B 292 GLN cc_start: 0.8670 (mt0) cc_final: 0.8330 (tp40) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.4191 time to fit residues: 43.0557 Evaluate side-chains 90 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.7597 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= 0.189 Angle : 0.524 5.337 3992 Z= 0.271 Chirality : 0.035 0.143 442 Planarity : 0.005 0.054 518 Dihedral : 4.056 17.074 394 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.32 % Allowed : 21.15 % Favored : 78.53 % 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: 2.05 (0.45), residues: 356 helix: 1.72 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.70 (0.66), residues: 107 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 0.012 0.001 PHE A 181 TYR 0.009 0.001 TYR B 162 ARG 0.012 0.001 ARG B 287 ********************** 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 89 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.528 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: A 162 TYR cc_start: 0.7290 (m-80) cc_final: 0.5833 (m-80) REVERT: A 218 MET cc_start: 0.9034 (tpp) cc_final: 0.8527 (tpt) REVERT: A 256 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7238 (ttm170) REVERT: A 264 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7576 (ttpt) REVERT: B 162 TYR cc_start: 0.6779 (t80) cc_final: 0.4956 (p90) REVERT: B 283 ARG cc_start: 0.7418 (ttm110) cc_final: 0.6799 (tpp80) REVERT: B 292 GLN cc_start: 0.8675 (mt0) cc_final: 0.8353 (tp40) outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.4238 time to fit residues: 42.4646 Evaluate side-chains 86 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN 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: 1.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.179151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147388 restraints weight = 13238.158| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 4.26 r_work: 0.3674 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2954 Z= 0.168 Angle : 0.512 5.284 3992 Z= 0.262 Chirality : 0.035 0.143 442 Planarity : 0.005 0.055 518 Dihedral : 3.929 16.662 394 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.96 % Allowed : 20.19 % Favored : 78.85 % 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: 2.17 (0.46), residues: 356 helix: 1.80 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.74 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.011 0.001 PHE A 181 TYR 0.009 0.001 TYR B 162 ARG 0.011 0.001 ARG B 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.74 seconds wall clock time: 41 minutes 14.32 seconds (2474.32 seconds total)