Starting phenix.real_space_refine on Wed Jul 23 16:22:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.map" model { file = "/net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knt_22962/07_2025/7knt_22962.cif" } resolution = 3.15 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= 0.037 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2443 2.51 5 N 614 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3716 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 920 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 3.07, per 1000 atoms: 0.83 Number of scatterers: 3716 At special positions: 0 Unit cell: (74.7, 97.94, 92.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 628 8.00 N 614 7.00 C 2443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 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: 1.01 Conformation dependent library (CDL) restraints added in 409.8 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 73.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.797A pdb=" N CYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 removed outlier: 5.862A pdb=" N GLU E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 81 Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.899A pdb=" N ARG E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 100 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.670A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.740A pdb=" N VAL E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 54 removed outlier: 3.671A pdb=" N ASN R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.679A pdb=" N CYS R 127 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 147 removed outlier: 4.086A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 removed outlier: 3.763A pdb=" N SER R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE R 153 " --> pdb=" O HIS R 149 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 198 removed outlier: 3.540A pdb=" N ASN R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE R 182 " --> pdb=" O LYS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.633A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.882A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY R 234 " --> pdb=" O MET R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 removed outlier: 3.517A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.575A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.619A pdb=" N ILE R 284 " --> pdb=" O ASN R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 319 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 340 removed outlier: 3.523A pdb=" N VAL R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 351 removed outlier: 3.736A pdb=" N LEU R 344 " --> pdb=" O ILE R 340 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 375 removed outlier: 3.516A pdb=" N HIS R 374 " --> pdb=" O HIS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 385 removed outlier: 3.642A pdb=" N LEU R 379 " --> pdb=" O PHE R 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 397 Processing sheet with id=AA1, first strand: chain 'R' and resid 86 through 87 removed outlier: 4.049A pdb=" N GLN R 86 " --> pdb=" O VAL R 101 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.88 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1133 1.35 - 1.47: 1021 1.47 - 1.59: 1627 1.59 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 3823 Sorted by residual: bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.53e+00 bond pdb=" N ILE R 293 " pdb=" CA ILE R 293 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.06e-02 8.90e+03 8.28e+00 bond pdb=" N ASP R 280 " pdb=" CA ASP R 280 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.30e+00 bond pdb=" N ARG R 274 " pdb=" CA ARG R 274 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+00 bond pdb=" N TYR R 277 " pdb=" CA TYR R 277 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.31e+00 ... (remaining 3818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 5148 2.91 - 5.82: 53 5.82 - 8.72: 4 8.72 - 11.63: 1 11.63 - 14.54: 1 Bond angle restraints: 5207 Sorted by residual: angle pdb=" CA LEU E 55 " pdb=" CB LEU E 55 " pdb=" CG LEU E 55 " ideal model delta sigma weight residual 116.30 130.84 -14.54 3.50e+00 8.16e-02 1.73e+01 angle pdb=" N ILE R 293 " pdb=" CA ILE R 293 " pdb=" C ILE R 293 " ideal model delta sigma weight residual 112.98 108.22 4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 113.01 108.50 4.51 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA ASN R 279 " pdb=" C ASN R 279 " pdb=" O ASN R 279 " ideal model delta sigma weight residual 122.37 118.10 4.27 1.15e+00 7.56e-01 1.38e+01 angle pdb=" N TRP R 283 " pdb=" CA TRP R 283 " pdb=" C TRP R 283 " ideal model delta sigma weight residual 112.86 108.76 4.10 1.22e+00 6.72e-01 1.13e+01 ... (remaining 5202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 1888 14.14 - 28.28: 219 28.28 - 42.42: 76 42.42 - 56.56: 15 56.56 - 70.70: 11 Dihedral angle restraints: 2209 sinusoidal: 869 harmonic: 1340 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 32.21 60.79 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -42.02 -43.98 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 74 " pdb=" CB CYS R 74 " ideal model delta sinusoidal sigma weight residual 93.00 51.75 41.25 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 2206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 420 0.043 - 0.087: 133 0.087 - 0.130: 21 0.130 - 0.174: 5 0.174 - 0.217: 6 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA THR R 288 " pdb=" N THR R 288 " pdb=" C THR R 288 " pdb=" CB THR R 288 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR R 292 " pdb=" N TYR R 292 " pdb=" C TYR R 292 " pdb=" CB TYR R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE R 293 " pdb=" CA ILE R 293 " pdb=" CG1 ILE R 293 " pdb=" CG2 ILE R 293 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 582 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 276 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU R 276 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU R 276 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR R 277 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 399 " 0.016 2.00e-02 2.50e+03 1.43e-02 5.10e+00 pdb=" CG TRP R 399 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 399 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 399 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 399 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 399 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 399 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 296 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO R 297 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 297 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 297 " -0.031 5.00e-02 4.00e+02 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 51 2.67 - 3.23: 3786 3.23 - 3.79: 5929 3.79 - 4.34: 8015 4.34 - 4.90: 12381 Nonbonded interactions: 30162 Sorted by model distance: nonbonded pdb=" OD2 ASP E 47 " pdb=" OG SER E 65 " model vdw 2.116 3.040 nonbonded pdb=" OD2 ASP R 96 " pdb=" OG SER R 98 " model vdw 2.257 3.040 nonbonded pdb=" O TYR R 46 " pdb=" NE2 GLN R 50 " model vdw 2.278 3.120 nonbonded pdb=" O ALA E 70 " pdb=" OG1 THR E 73 " model vdw 2.353 3.040 nonbonded pdb=" OD2 ASP R 70 " pdb=" OH TYR R 124 " model vdw 2.381 3.040 ... (remaining 30157 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.004 0.034 3829 Z= 0.251 Angle : 0.760 14.540 5219 Z= 0.460 Chirality : 0.045 0.217 585 Planarity : 0.004 0.056 637 Dihedral : 14.556 70.696 1323 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.74 % Allowed : 0.99 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.48 (0.40), residues: 443 helix: 0.22 (0.32), residues: 287 sheet: -0.67 (1.82), residues: 12 loop : -1.22 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 399 HIS 0.004 0.001 HIS R 370 PHE 0.011 0.001 PHE E 44 TYR 0.013 0.001 TYR E 32 ARG 0.011 0.001 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.26961 ( 206) hydrogen bonds : angle 8.26399 ( 612) SS BOND : bond 0.00352 ( 6) SS BOND : angle 2.31683 ( 12) covalent geometry : bond 0.00390 ( 3823) covalent geometry : angle 0.75283 ( 5207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: R 38 ARG cc_start: 0.8606 (mmm160) cc_final: 0.8311 (mmm160) REVERT: R 42 MET cc_start: 0.8034 (tpp) cc_final: 0.7791 (tpt) REVERT: R 46 TYR cc_start: 0.7583 (t80) cc_final: 0.7299 (t80) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1763 time to fit residues: 15.2219 Evaluate side-chains 56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.111456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.084981 restraints weight = 9997.843| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.59 r_work: 0.3533 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3829 Z= 0.199 Angle : 0.721 13.312 5219 Z= 0.372 Chirality : 0.045 0.166 585 Planarity : 0.005 0.041 637 Dihedral : 4.991 29.434 493 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.46 % Allowed : 11.11 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.22 (0.40), residues: 443 helix: 0.31 (0.30), residues: 290 sheet: -0.77 (1.77), residues: 12 loop : -0.84 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 399 HIS 0.004 0.001 HIS R 295 PHE 0.013 0.001 PHE R 308 TYR 0.017 0.002 TYR R 46 ARG 0.002 0.000 ARG R 38 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 206) hydrogen bonds : angle 5.32526 ( 612) SS BOND : bond 0.00494 ( 6) SS BOND : angle 2.47357 ( 12) covalent geometry : bond 0.00446 ( 3823) covalent geometry : angle 0.71198 ( 5207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: R 46 TYR cc_start: 0.7848 (t80) cc_final: 0.7235 (t80) REVERT: R 87 LEU cc_start: 0.8235 (pt) cc_final: 0.8030 (mt) REVERT: R 280 ASP cc_start: 0.8249 (t0) cc_final: 0.8049 (t0) REVERT: R 292 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7471 (t80) outliers start: 14 outliers final: 12 residues processed: 73 average time/residue: 0.2018 time to fit residues: 17.7867 Evaluate side-chains 63 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 333 LYS Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.110836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.084705 restraints weight = 9818.512| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.63 r_work: 0.3534 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3829 Z= 0.171 Angle : 0.692 13.926 5219 Z= 0.340 Chirality : 0.043 0.143 585 Planarity : 0.005 0.044 637 Dihedral : 4.650 17.025 491 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.69 % Allowed : 14.32 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.17 (0.40), residues: 443 helix: 0.38 (0.29), residues: 297 sheet: -0.46 (1.83), residues: 12 loop : -1.00 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 399 HIS 0.005 0.001 HIS R 370 PHE 0.012 0.001 PHE R 228 TYR 0.011 0.002 TYR R 46 ARG 0.003 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 206) hydrogen bonds : angle 4.88518 ( 612) SS BOND : bond 0.00461 ( 6) SS BOND : angle 1.76125 ( 12) covalent geometry : bond 0.00391 ( 3823) covalent geometry : angle 0.68745 ( 5207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.456 Fit side-chains REVERT: E 71 ASP cc_start: 0.8657 (m-30) cc_final: 0.8350 (p0) REVERT: E 76 MET cc_start: 0.8693 (mmm) cc_final: 0.7931 (mmm) REVERT: R 46 TYR cc_start: 0.7996 (t80) cc_final: 0.7493 (t80) REVERT: R 87 LEU cc_start: 0.8275 (pt) cc_final: 0.8066 (mt) REVERT: R 292 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7505 (t80) REVERT: R 369 MET cc_start: 0.8392 (tpp) cc_final: 0.8162 (tpt) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.1980 time to fit residues: 16.2453 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 333 LYS Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 279 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.112254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.086110 restraints weight = 9803.630| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.64 r_work: 0.3559 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3829 Z= 0.134 Angle : 0.625 12.115 5219 Z= 0.315 Chirality : 0.040 0.153 585 Planarity : 0.005 0.043 637 Dihedral : 4.498 15.988 491 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.94 % Allowed : 15.80 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.02 (0.40), residues: 443 helix: 0.56 (0.29), residues: 300 sheet: -0.24 (1.88), residues: 12 loop : -1.06 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 399 HIS 0.004 0.001 HIS R 370 PHE 0.009 0.001 PHE R 228 TYR 0.013 0.001 TYR E 32 ARG 0.003 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 206) hydrogen bonds : angle 4.60245 ( 612) SS BOND : bond 0.00399 ( 6) SS BOND : angle 1.37611 ( 12) covalent geometry : bond 0.00303 ( 3823) covalent geometry : angle 0.62223 ( 5207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.452 Fit side-chains REVERT: E 48 MET cc_start: 0.8966 (mmm) cc_final: 0.8694 (mmm) REVERT: E 71 ASP cc_start: 0.8695 (m-30) cc_final: 0.7820 (t70) REVERT: R 46 TYR cc_start: 0.8003 (t80) cc_final: 0.7623 (t80) REVERT: R 87 LEU cc_start: 0.8266 (pt) cc_final: 0.8043 (mt) REVERT: R 292 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7576 (t80) REVERT: R 369 MET cc_start: 0.8405 (tpp) cc_final: 0.8145 (tpt) REVERT: R 373 MET cc_start: 0.8967 (mtm) cc_final: 0.8764 (mtm) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.1869 time to fit residues: 15.7530 Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 333 LYS Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.112795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086483 restraints weight = 9955.469| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.67 r_work: 0.3569 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3829 Z= 0.130 Angle : 0.606 10.822 5219 Z= 0.306 Chirality : 0.040 0.118 585 Planarity : 0.004 0.041 637 Dihedral : 4.391 13.266 491 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.19 % Allowed : 16.05 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.22 (0.40), residues: 443 helix: 0.74 (0.30), residues: 299 sheet: -0.08 (1.91), residues: 12 loop : -1.06 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 399 HIS 0.003 0.001 HIS R 238 PHE 0.008 0.001 PHE R 228 TYR 0.012 0.001 TYR R 46 ARG 0.003 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 206) hydrogen bonds : angle 4.42599 ( 612) SS BOND : bond 0.00685 ( 6) SS BOND : angle 1.23538 ( 12) covalent geometry : bond 0.00292 ( 3823) covalent geometry : angle 0.60399 ( 5207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.406 Fit side-chains REVERT: E 71 ASP cc_start: 0.8624 (m-30) cc_final: 0.7727 (t70) REVERT: E 102 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7952 (tpp80) REVERT: R 87 LEU cc_start: 0.8272 (pt) cc_final: 0.8039 (mt) REVERT: R 292 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7582 (t80) REVERT: R 369 MET cc_start: 0.8443 (tpp) cc_final: 0.8195 (tpt) outliers start: 21 outliers final: 14 residues processed: 72 average time/residue: 0.2028 time to fit residues: 17.4280 Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 333 LYS Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 348 GLU Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.113114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086636 restraints weight = 9841.955| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.63 r_work: 0.3573 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3829 Z= 0.124 Angle : 0.602 9.604 5219 Z= 0.302 Chirality : 0.039 0.115 585 Planarity : 0.004 0.040 637 Dihedral : 4.254 15.018 491 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.94 % Allowed : 17.78 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.29 (0.40), residues: 443 helix: 0.79 (0.30), residues: 299 sheet: 0.21 (1.94), residues: 12 loop : -1.04 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 399 HIS 0.003 0.001 HIS R 238 PHE 0.009 0.001 PHE E 92 TYR 0.024 0.002 TYR R 46 ARG 0.003 0.000 ARG E 102 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 206) hydrogen bonds : angle 4.31248 ( 612) SS BOND : bond 0.00601 ( 6) SS BOND : angle 1.43881 ( 12) covalent geometry : bond 0.00284 ( 3823) covalent geometry : angle 0.59844 ( 5207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.484 Fit side-chains REVERT: E 48 MET cc_start: 0.8913 (mmm) cc_final: 0.8704 (mmm) REVERT: E 71 ASP cc_start: 0.8629 (m-30) cc_final: 0.7729 (t70) REVERT: R 87 LEU cc_start: 0.8241 (pt) cc_final: 0.8014 (mt) REVERT: R 99 GLU cc_start: 0.7152 (pp20) cc_final: 0.6864 (pp20) REVERT: R 292 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7600 (t80) REVERT: R 369 MET cc_start: 0.8382 (tpp) cc_final: 0.8087 (tpt) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.2033 time to fit residues: 16.5454 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 333 LYS Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.113463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.087435 restraints weight = 9816.874| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.63 r_work: 0.3584 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3829 Z= 0.124 Angle : 0.630 9.274 5219 Z= 0.316 Chirality : 0.041 0.264 585 Planarity : 0.004 0.042 637 Dihedral : 4.332 16.481 491 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.44 % Allowed : 19.75 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.42 (0.40), residues: 443 helix: 0.89 (0.30), residues: 298 sheet: 0.19 (1.93), residues: 12 loop : -0.99 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 399 HIS 0.003 0.001 HIS R 238 PHE 0.007 0.001 PHE R 228 TYR 0.016 0.001 TYR R 46 ARG 0.002 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 206) hydrogen bonds : angle 4.22824 ( 612) SS BOND : bond 0.00329 ( 6) SS BOND : angle 3.01125 ( 12) covalent geometry : bond 0.00286 ( 3823) covalent geometry : angle 0.61411 ( 5207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.417 Fit side-chains REVERT: E 48 MET cc_start: 0.8997 (mmm) cc_final: 0.8733 (mmm) REVERT: E 71 ASP cc_start: 0.8605 (m-30) cc_final: 0.7789 (t70) REVERT: E 122 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: R 87 LEU cc_start: 0.8211 (pt) cc_final: 0.7979 (mt) REVERT: R 292 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7666 (t80) REVERT: R 373 MET cc_start: 0.8809 (mtm) cc_final: 0.8561 (mtm) outliers start: 18 outliers final: 13 residues processed: 65 average time/residue: 0.1860 time to fit residues: 14.6678 Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.112335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086011 restraints weight = 9903.523| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.70 r_work: 0.3558 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3829 Z= 0.132 Angle : 0.628 8.795 5219 Z= 0.316 Chirality : 0.041 0.206 585 Planarity : 0.004 0.039 637 Dihedral : 4.360 16.609 491 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.20 % Allowed : 20.25 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.45 (0.40), residues: 443 helix: 0.84 (0.30), residues: 299 sheet: 0.65 (1.93), residues: 12 loop : -0.85 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 84 HIS 0.003 0.001 HIS R 238 PHE 0.008 0.001 PHE R 228 TYR 0.013 0.002 TYR E 32 ARG 0.003 0.000 ARG E 102 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 206) hydrogen bonds : angle 4.16014 ( 612) SS BOND : bond 0.00323 ( 6) SS BOND : angle 2.78842 ( 12) covalent geometry : bond 0.00311 ( 3823) covalent geometry : angle 0.61451 ( 5207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.472 Fit side-chains REVERT: E 71 ASP cc_start: 0.8607 (m-30) cc_final: 0.7744 (t70) REVERT: E 122 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: R 87 LEU cc_start: 0.8256 (pt) cc_final: 0.8013 (mt) REVERT: R 292 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7580 (t80) REVERT: R 373 MET cc_start: 0.8830 (mtm) cc_final: 0.8607 (mtm) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.2506 time to fit residues: 20.4292 Evaluate side-chains 66 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.111560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085377 restraints weight = 9894.461| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.69 r_work: 0.3545 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3829 Z= 0.147 Angle : 0.631 8.455 5219 Z= 0.318 Chirality : 0.041 0.179 585 Planarity : 0.004 0.039 637 Dihedral : 4.400 16.292 491 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.70 % Allowed : 20.49 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.39 (0.40), residues: 443 helix: 0.77 (0.30), residues: 299 sheet: 0.74 (1.89), residues: 12 loop : -0.80 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 84 HIS 0.004 0.001 HIS R 370 PHE 0.008 0.001 PHE R 228 TYR 0.014 0.002 TYR E 32 ARG 0.003 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 206) hydrogen bonds : angle 4.21562 ( 612) SS BOND : bond 0.00328 ( 6) SS BOND : angle 2.32125 ( 12) covalent geometry : bond 0.00349 ( 3823) covalent geometry : angle 0.62217 ( 5207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.527 Fit side-chains REVERT: E 48 MET cc_start: 0.8840 (mmm) cc_final: 0.8618 (mmm) REVERT: E 71 ASP cc_start: 0.8586 (m-30) cc_final: 0.7789 (t70) REVERT: E 122 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: R 373 MET cc_start: 0.8824 (mtm) cc_final: 0.8607 (mtm) outliers start: 15 outliers final: 14 residues processed: 62 average time/residue: 0.1846 time to fit residues: 14.2383 Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0010 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.112600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086593 restraints weight = 9887.732| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.70 r_work: 0.3572 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3829 Z= 0.126 Angle : 0.629 8.360 5219 Z= 0.314 Chirality : 0.041 0.178 585 Planarity : 0.004 0.041 637 Dihedral : 4.354 16.283 491 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.46 % Allowed : 20.99 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.56 (0.40), residues: 443 helix: 0.94 (0.30), residues: 299 sheet: 0.46 (1.88), residues: 12 loop : -0.83 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 84 HIS 0.003 0.001 HIS R 238 PHE 0.007 0.001 PHE R 228 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 206) hydrogen bonds : angle 4.13513 ( 612) SS BOND : bond 0.00313 ( 6) SS BOND : angle 2.22194 ( 12) covalent geometry : bond 0.00294 ( 3823) covalent geometry : angle 0.62093 ( 5207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.855 Fit side-chains REVERT: E 48 MET cc_start: 0.8831 (mmm) cc_final: 0.8587 (mmm) REVERT: E 71 ASP cc_start: 0.8554 (m-30) cc_final: 0.7776 (t70) REVERT: E 122 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: R 87 LEU cc_start: 0.8402 (pt) cc_final: 0.8068 (mt) REVERT: R 292 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7585 (t80) outliers start: 14 outliers final: 12 residues processed: 61 average time/residue: 0.2155 time to fit residues: 16.6014 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.112860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086441 restraints weight = 9906.566| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.70 r_work: 0.3568 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3829 Z= 0.127 Angle : 0.632 8.589 5219 Z= 0.314 Chirality : 0.041 0.160 585 Planarity : 0.004 0.040 637 Dihedral : 4.325 18.266 491 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.70 % Allowed : 21.23 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.60 (0.40), residues: 443 helix: 1.00 (0.30), residues: 299 sheet: 0.28 (1.82), residues: 12 loop : -0.86 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 84 HIS 0.003 0.001 HIS R 370 PHE 0.007 0.001 PHE R 228 TYR 0.017 0.002 TYR E 32 ARG 0.003 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 206) hydrogen bonds : angle 4.06468 ( 612) SS BOND : bond 0.00285 ( 6) SS BOND : angle 2.09152 ( 12) covalent geometry : bond 0.00296 ( 3823) covalent geometry : angle 0.62479 ( 5207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.54 seconds wall clock time: 60 minutes 30.98 seconds (3630.98 seconds total)