Starting phenix.real_space_refine on Thu Nov 14 09:10:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/11_2024/8exr_28660.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 5 5.49 5 S 20 5.16 5 C 3438 2.51 5 N 802 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5111 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2496 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 6, 'TRANS': 288} Chain breaks: 1 Chain: "A" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 2051 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.01, per 1000 atoms: 0.78 Number of scatterers: 5111 At special positions: 0 Unit cell: (72.38, 85.47, 93.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 20 16.00 P 5 15.00 O 844 8.00 N 802 7.00 C 3438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 575.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 70.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.858A pdb=" N TYR B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 48 removed outlier: 4.065A pdb=" N LEU B 43 " --> pdb=" O TRP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 100 through 133 removed outlier: 4.624A pdb=" N VAL B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.327A pdb=" N LEU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.197A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 251 removed outlier: 3.501A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 329 removed outlier: 3.534A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.125A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.566A pdb=" N VAL A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.814A pdb=" N ASN A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.857A pdb=" N HIS A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 253 No H-bonds generated for 'chain 'A' and resid 252 through 253' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.752A pdb=" N VAL A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.734A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 329 removed outlier: 4.354A pdb=" N LEU C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.040A pdb=" N THR C 335 " --> pdb=" O GLN C 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.685A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 870 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: 1.44 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1301 1.33 - 1.47: 1570 1.47 - 1.61: 2315 1.61 - 1.75: 3 1.75 - 1.89: 34 Bond restraints: 5223 Sorted by residual: bond pdb=" CB HIS B 213 " pdb=" CG HIS B 213 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.05e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" CB PHE A 173 " pdb=" CG PHE A 173 " ideal model delta sigma weight residual 1.502 1.321 0.181 2.30e-02 1.89e+03 6.18e+01 bond pdb=" NE1 TRP B 39 " pdb=" CE2 TRP B 39 " ideal model delta sigma weight residual 1.370 1.285 0.085 1.10e-02 8.26e+03 6.00e+01 bond pdb=" CB HIS A 205 " pdb=" CG HIS A 205 " ideal model delta sigma weight residual 1.497 1.389 0.108 1.40e-02 5.10e+03 5.93e+01 ... (remaining 5218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 6387 3.28 - 6.57: 574 6.57 - 9.85: 51 9.85 - 13.13: 6 13.13 - 16.42: 3 Bond angle restraints: 7021 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 108.46 122.06 -13.60 1.49e+00 4.50e-01 8.33e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 114.04 102.97 11.07 1.24e+00 6.50e-01 7.97e+01 angle pdb=" N VAL B 160 " pdb=" CA VAL B 160 " pdb=" C VAL B 160 " ideal model delta sigma weight residual 108.46 121.66 -13.20 1.49e+00 4.50e-01 7.84e+01 angle pdb=" CA PHE B 30 " pdb=" CB PHE B 30 " pdb=" CG PHE B 30 " ideal model delta sigma weight residual 113.80 105.18 8.62 1.00e+00 1.00e+00 7.44e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 110.56 126.98 -16.42 1.94e+00 2.66e-01 7.16e+01 ... (remaining 7016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 2907 14.09 - 28.17: 148 28.17 - 42.25: 49 42.25 - 56.34: 30 56.34 - 70.42: 11 Dihedral angle restraints: 3145 sinusoidal: 1362 harmonic: 1783 Sorted by residual: dihedral pdb=" C PHE B 258 " pdb=" N PHE B 258 " pdb=" CA PHE B 258 " pdb=" CB PHE B 258 " ideal model delta harmonic sigma weight residual -122.60 -114.82 -7.78 0 2.50e+00 1.60e-01 9.68e+00 dihedral pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " ideal model delta harmonic sigma weight residual 122.80 130.57 -7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" CG ARG A 235 " pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " ideal model delta sinusoidal sigma weight residual 180.00 143.09 36.91 2 1.50e+01 4.44e-03 7.69e+00 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 564 0.117 - 0.234: 200 0.234 - 0.351: 31 0.351 - 0.468: 4 0.468 - 0.584: 1 Chirality restraints: 800 Sorted by residual: chirality pdb=" C5 P6L A 702 " pdb=" C6 P6L A 702 " pdb=" C7 P6L A 702 " pdb=" O4 P6L A 702 " both_signs ideal model delta sigma weight residual False -2.31 -1.73 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" CA TRP B 174 " pdb=" N TRP B 174 " pdb=" C TRP B 174 " pdb=" CB TRP B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR B 155 " pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CB TYR B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 797 not shown) Planarity restraints: 823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 P6L B 702 " 0.079 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C22 P6L B 702 " -0.213 2.00e-02 2.50e+03 pdb=" C23 P6L B 702 " 0.213 2.00e-02 2.50e+03 pdb=" C24 P6L B 702 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 P6L A 702 " 0.077 2.00e-02 2.50e+03 1.53e-01 2.35e+02 pdb=" C22 P6L A 702 " -0.203 2.00e-02 2.50e+03 pdb=" C23 P6L A 702 " 0.203 2.00e-02 2.50e+03 pdb=" C24 P6L A 702 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 P6L A 702 " -0.074 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" C33 P6L A 702 " 0.195 2.00e-02 2.50e+03 pdb=" C34 P6L A 702 " -0.195 2.00e-02 2.50e+03 pdb=" C35 P6L A 702 " 0.074 2.00e-02 2.50e+03 ... (remaining 820 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 76 2.59 - 3.17: 5122 3.17 - 3.75: 7615 3.75 - 4.32: 10357 4.32 - 4.90: 15033 Nonbonded interactions: 38203 Sorted by model distance: nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.016 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.017 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.038 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.050 2.230 nonbonded pdb=" O GLY B 286 " pdb=" CG LYS B 287 " model vdw 2.142 3.440 ... (remaining 38198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.026 0.181 5223 Z= 1.652 Angle : 1.944 16.416 7021 Z= 1.328 Chirality : 0.115 0.584 800 Planarity : 0.013 0.161 823 Dihedral : 12.156 70.423 1981 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.76 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.66 (0.32), residues: 580 helix: -0.13 (0.24), residues: 383 sheet: -0.25 (0.87), residues: 26 loop : -0.87 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP B 99 HIS 0.012 0.003 HIS A 153 PHE 0.033 0.006 PHE B 284 TYR 0.099 0.012 TYR A 203 ARG 0.006 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt) REVERT: B 136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp) REVERT: B 255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm) REVERT: A 141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0) REVERT: A 187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80) REVERT: A 219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt) REVERT: A 276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40) REVERT: C 295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2046 time to fit residues: 47.6046 Evaluate side-chains 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN A 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5223 Z= 0.228 Angle : 0.726 6.862 7021 Z= 0.412 Chirality : 0.045 0.211 800 Planarity : 0.005 0.052 823 Dihedral : 13.281 71.980 725 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.07 % Rotamer: Outliers : 3.01 % Allowed : 12.06 % Favored : 84.93 % 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: 0.99 (0.34), residues: 580 helix: 1.41 (0.25), residues: 375 sheet: -0.04 (0.98), residues: 35 loop : -0.81 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 110 HIS 0.005 0.001 HIS B 213 PHE 0.026 0.002 PHE B 16 TYR 0.020 0.002 TYR B 127 ARG 0.005 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 MET cc_start: 0.7183 (mmt) cc_final: 0.6843 (ptp) REVERT: B 136 LEU cc_start: 0.6829 (tp) cc_final: 0.6393 (mp) REVERT: B 168 GLN cc_start: 0.6419 (mp10) cc_final: 0.6196 (mm-40) REVERT: B 240 ASP cc_start: 0.8057 (m-30) cc_final: 0.7853 (t0) REVERT: B 319 PHE cc_start: 0.7657 (t80) cc_final: 0.7440 (t80) REVERT: A 122 LEU cc_start: 0.8219 (mt) cc_final: 0.7984 (tp) REVERT: C 295 LEU cc_start: 0.8422 (mt) cc_final: 0.7838 (tt) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.1663 time to fit residues: 34.5969 Evaluate side-chains 120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 328 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5223 Z= 0.200 Angle : 0.656 10.997 7021 Z= 0.356 Chirality : 0.043 0.195 800 Planarity : 0.004 0.052 823 Dihedral : 11.980 88.540 725 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.08 % Allowed : 15.07 % Favored : 80.85 % 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: 0.99 (0.34), residues: 580 helix: 1.48 (0.25), residues: 380 sheet: -0.35 (1.08), residues: 32 loop : -1.00 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 174 HIS 0.003 0.001 HIS B 213 PHE 0.020 0.002 PHE C 328 TYR 0.018 0.002 TYR A 261 ARG 0.004 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: B 136 LEU cc_start: 0.6956 (tp) cc_final: 0.6688 (mp) REVERT: B 266 MET cc_start: 0.6645 (tpt) cc_final: 0.6358 (tpt) REVERT: A 22 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (t80) REVERT: A 122 LEU cc_start: 0.8326 (mt) cc_final: 0.8118 (tp) REVERT: A 165 GLU cc_start: 0.6592 (pm20) cc_final: 0.6337 (pt0) REVERT: C 300 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8357 (tm-30) outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 0.1558 time to fit residues: 29.2245 Evaluate side-chains 127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 328 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5223 Z= 0.248 Angle : 0.675 8.854 7021 Z= 0.372 Chirality : 0.044 0.184 800 Planarity : 0.005 0.052 823 Dihedral : 11.720 89.583 725 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.96 % Allowed : 16.84 % Favored : 78.19 % 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: 0.74 (0.34), residues: 580 helix: 1.50 (0.26), residues: 372 sheet: -0.72 (0.94), residues: 37 loop : -1.47 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.036 0.002 PHE B 22 TYR 0.026 0.002 TYR A 186 ARG 0.003 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASN cc_start: 0.6650 (m110) cc_final: 0.6242 (m-40) REVERT: A 7 MET cc_start: 0.7121 (mtm) cc_final: 0.6898 (mtm) REVERT: A 122 LEU cc_start: 0.8424 (mt) cc_final: 0.8196 (tp) REVERT: A 246 ASP cc_start: 0.7143 (t0) cc_final: 0.6719 (t0) REVERT: C 325 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8194 (tm-30) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.1510 time to fit residues: 27.5691 Evaluate side-chains 132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5223 Z= 0.202 Angle : 0.651 8.881 7021 Z= 0.356 Chirality : 0.044 0.220 800 Planarity : 0.005 0.057 823 Dihedral : 11.132 84.401 725 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.61 % Allowed : 18.97 % Favored : 76.42 % 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: 0.71 (0.34), residues: 580 helix: 1.56 (0.26), residues: 374 sheet: -0.97 (0.91), residues: 37 loop : -1.69 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.050 0.002 PHE B 22 TYR 0.021 0.002 TYR A 186 ARG 0.002 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 285 ASN cc_start: 0.6794 (m110) cc_final: 0.6292 (m-40) REVERT: A 22 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6958 (t80) REVERT: A 123 LYS cc_start: 0.8186 (tttt) cc_final: 0.7936 (pttm) outliers start: 26 outliers final: 17 residues processed: 135 average time/residue: 0.1529 time to fit residues: 27.3460 Evaluate side-chains 130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5223 Z= 0.181 Angle : 0.606 10.819 7021 Z= 0.328 Chirality : 0.042 0.195 800 Planarity : 0.005 0.057 823 Dihedral : 10.288 73.269 725 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.90 % Allowed : 21.10 % Favored : 75.00 % 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: 1.01 (0.35), residues: 580 helix: 1.76 (0.26), residues: 367 sheet: -1.05 (0.93), residues: 36 loop : -1.29 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 174 HIS 0.002 0.001 HIS B 213 PHE 0.043 0.002 PHE B 22 TYR 0.018 0.002 TYR B 127 ARG 0.007 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: B 203 TYR cc_start: 0.6710 (t80) cc_final: 0.6312 (t80) REVERT: B 266 MET cc_start: 0.6563 (tpt) cc_final: 0.6316 (tpt) REVERT: B 285 ASN cc_start: 0.6398 (m110) cc_final: 0.5906 (m-40) REVERT: A 7 MET cc_start: 0.6806 (mtm) cc_final: 0.6534 (mtm) REVERT: A 22 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6802 (t80) REVERT: A 142 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6539 (mt-10) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.1503 time to fit residues: 26.8714 Evaluate side-chains 125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 0.0070 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 0.0570 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5223 Z= 0.170 Angle : 0.615 14.575 7021 Z= 0.322 Chirality : 0.042 0.165 800 Planarity : 0.004 0.055 823 Dihedral : 10.000 79.047 725 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.90 % Allowed : 21.63 % Favored : 74.47 % 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: 1.03 (0.35), residues: 580 helix: 1.83 (0.26), residues: 366 sheet: -0.98 (0.95), residues: 36 loop : -1.43 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 174 HIS 0.003 0.001 HIS B 213 PHE 0.038 0.002 PHE B 22 TYR 0.015 0.001 TYR A 261 ARG 0.006 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ARG cc_start: 0.6246 (ttt180) cc_final: 0.6036 (ttt90) REVERT: B 266 MET cc_start: 0.6522 (tpt) cc_final: 0.6283 (tpt) REVERT: B 285 ASN cc_start: 0.6403 (m110) cc_final: 0.6051 (m-40) REVERT: A 7 MET cc_start: 0.6708 (mtm) cc_final: 0.6239 (mtm) REVERT: A 22 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6868 (t80) REVERT: A 271 ASN cc_start: 0.6323 (m-40) cc_final: 0.6097 (p0) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.1581 time to fit residues: 25.9286 Evaluate side-chains 126 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5223 Z= 0.160 Angle : 0.592 14.017 7021 Z= 0.310 Chirality : 0.041 0.170 800 Planarity : 0.004 0.050 823 Dihedral : 9.722 85.643 725 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.72 % Allowed : 22.34 % Favored : 73.94 % 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: 0.89 (0.35), residues: 580 helix: 1.83 (0.26), residues: 373 sheet: -1.06 (0.96), residues: 36 loop : -1.90 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 174 HIS 0.003 0.001 HIS B 213 PHE 0.030 0.001 PHE B 22 TYR 0.014 0.001 TYR A 261 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7288 (mt) REVERT: B 266 MET cc_start: 0.6493 (tpt) cc_final: 0.6272 (tpt) REVERT: A 7 MET cc_start: 0.6665 (mtm) cc_final: 0.6204 (mtm) REVERT: A 22 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6809 (t80) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.1656 time to fit residues: 28.4097 Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 271 ASN A 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5223 Z= 0.194 Angle : 0.676 15.189 7021 Z= 0.355 Chirality : 0.043 0.170 800 Planarity : 0.004 0.049 823 Dihedral : 9.890 89.565 725 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.55 % Allowed : 24.29 % Favored : 72.16 % 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: 0.72 (0.34), residues: 580 helix: 1.67 (0.26), residues: 374 sheet: -1.01 (0.96), residues: 36 loop : -1.96 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 174 HIS 0.006 0.001 HIS B 213 PHE 0.048 0.002 PHE B 22 TYR 0.014 0.002 TYR A 261 ARG 0.006 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7294 (mt) REVERT: B 255 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7455 (mptt) REVERT: A 7 MET cc_start: 0.6715 (mtm) cc_final: 0.6232 (mtm) REVERT: A 22 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6855 (t80) REVERT: A 123 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (pttm) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.1535 time to fit residues: 24.6736 Evaluate side-chains 122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5223 Z= 0.185 Angle : 0.670 15.772 7021 Z= 0.349 Chirality : 0.043 0.176 800 Planarity : 0.004 0.051 823 Dihedral : 9.768 87.898 725 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.37 % Allowed : 24.47 % Favored : 72.16 % 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: 0.64 (0.35), residues: 580 helix: 1.60 (0.26), residues: 378 sheet: -1.13 (0.95), residues: 36 loop : -2.02 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.044 0.002 PHE B 22 TYR 0.021 0.002 TYR B 175 ARG 0.006 0.001 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7296 (mt) REVERT: B 255 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7465 (mmtm) REVERT: B 266 MET cc_start: 0.6588 (tpt) cc_final: 0.6323 (tpt) REVERT: A 7 MET cc_start: 0.6710 (mtm) cc_final: 0.6258 (mtm) REVERT: A 22 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6874 (t80) REVERT: A 123 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7613 (tptp) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1578 time to fit residues: 25.4669 Evaluate side-chains 125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 325 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.188141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.167451 restraints weight = 10011.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171770 restraints weight = 6063.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.174776 restraints weight = 4120.496| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5223 Z= 0.176 Angle : 0.643 10.513 7021 Z= 0.340 Chirality : 0.043 0.167 800 Planarity : 0.004 0.049 823 Dihedral : 9.555 88.309 725 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.37 % Allowed : 24.82 % Favored : 71.81 % 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: 0.69 (0.35), residues: 580 helix: 1.61 (0.26), residues: 376 sheet: -1.17 (0.97), residues: 36 loop : -1.88 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 PHE 0.031 0.001 PHE B 22 TYR 0.017 0.002 TYR B 175 ARG 0.006 0.001 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.21 seconds wall clock time: 26 minutes 48.47 seconds (1608.47 seconds total)