Starting phenix.real_space_refine on Tue Feb 11 02:30:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knt_22962/02_2025/7knt_22962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knt_22962/02_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_22962/02_2025/7knt_22962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knt_22962/02_2025/7knt_22962.map" model { file = "/net/cci-nas-00/data/ceres_data/7knt_22962/02_2025/7knt_22962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knt_22962/02_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-5592/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: 2.89, per 1000 atoms: 0.78 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: 0.89 Conformation dependent library (CDL) restraints added in 439.2 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: 0.38 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: 1.00 Time building geometry restraints manager: 1.07 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: 0.600 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- 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 3823 Z= 0.246 Angle : 0.753 14.540 5207 Z= 0.458 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 *********************** 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 : 0.434 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: 0.1800 time to fit residues: 15.5585 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 : 0.400 ------------------------------------------------------------------------------- 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 = 0.084980 restraints weight = 9997.844| |-----------------------------------------------------------------------------| 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 3823 Z= 0.293 Angle : 0.712 13.312 5207 Z= 0.369 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 *********************** 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 : 0.380 Fit side-chains revert: symmetry clash REVERT: R 46 TYR cc_start: 0.7847 (t80) cc_final: 0.7235 (t80) REVERT: R 87 LEU cc_start: 0.8234 (pt) cc_final: 0.8029 (mt) REVERT: R 280 ASP cc_start: 0.8250 (t0) cc_final: 0.8049 (t0) REVERT: R 292 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7472 (t80) outliers start: 14 outliers final: 12 residues processed: 73 average time/residue: 0.1986 time to fit residues: 17.4306 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 : 0.424 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 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 = 0.4142 r_free = 0.4142 target = 0.112031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.086082 restraints weight = 9759.746| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.64 r_work: 0.3556 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3823 Z= 0.215 Angle : 0.662 13.765 5207 Z= 0.326 Chirality : 0.041 0.132 585 Planarity : 0.005 0.043 637 Dihedral : 4.578 17.254 491 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.69 % Allowed : 14.81 % Favored : 80.49 % 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: -0.08 (0.40), residues: 443 helix: 0.46 (0.29), residues: 299 sheet: -0.41 (1.83), residues: 12 loop : -1.02 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 399 HIS 0.004 0.001 HIS R 370 PHE 0.011 0.001 PHE R 228 TYR 0.011 0.001 TYR E 32 ARG 0.002 0.000 ARG R 113 *********************** 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 : 0.448 Fit side-chains REVERT: E 71 ASP cc_start: 0.8660 (m-30) cc_final: 0.8369 (p0) REVERT: E 76 MET cc_start: 0.8698 (mmm) cc_final: 0.7978 (mmm) REVERT: R 46 TYR cc_start: 0.7940 (t80) cc_final: 0.7476 (t80) REVERT: R 87 LEU cc_start: 0.8276 (pt) cc_final: 0.8067 (mt) REVERT: R 292 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7514 (t80) REVERT: R 369 MET cc_start: 0.8395 (tpp) cc_final: 0.8144 (tpt) outliers start: 19 outliers final: 14 residues processed: 69 average time/residue: 0.1962 time to fit residues: 16.2099 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.112962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.086821 restraints weight = 9767.017| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.63 r_work: 0.3577 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3823 Z= 0.187 Angle : 0.620 12.499 5207 Z= 0.311 Chirality : 0.040 0.147 585 Planarity : 0.004 0.041 637 Dihedral : 4.432 16.177 491 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.20 % Allowed : 16.05 % Favored : 79.75 % 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: 0.09 (0.40), residues: 443 helix: 0.62 (0.30), residues: 300 sheet: -0.19 (1.88), residues: 12 loop : -1.05 (0.55), residues: 131 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 E 32 ARG 0.003 0.000 ARG E 112 *********************** 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 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.369 Fit side-chains REVERT: E 48 MET cc_start: 0.8932 (mmm) cc_final: 0.8663 (mmm) REVERT: E 71 ASP cc_start: 0.8654 (m-30) cc_final: 0.7766 (t70) REVERT: R 46 TYR cc_start: 0.7942 (t80) cc_final: 0.7630 (t80) REVERT: R 87 LEU cc_start: 0.8279 (pt) cc_final: 0.8060 (mt) REVERT: R 292 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7588 (t80) REVERT: R 369 MET cc_start: 0.8410 (tpp) cc_final: 0.8147 (tpt) outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.1829 time to fit residues: 15.0660 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 : 0.431 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.113572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087129 restraints weight = 9903.433| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.68 r_work: 0.3581 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3823 Z= 0.189 Angle : 0.603 11.337 5207 Z= 0.305 Chirality : 0.039 0.116 585 Planarity : 0.004 0.041 637 Dihedral : 4.354 14.883 491 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.69 % Allowed : 17.53 % Favored : 77.78 % 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: 0.24 (0.40), residues: 443 helix: 0.73 (0.30), residues: 299 sheet: -0.06 (1.90), residues: 12 loop : -1.00 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 399 HIS 0.003 0.001 HIS R 238 PHE 0.007 0.001 PHE R 228 TYR 0.011 0.001 TYR R 91 ARG 0.002 0.000 ARG R 113 *********************** 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 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.447 Fit side-chains REVERT: E 71 ASP cc_start: 0.8632 (m-30) cc_final: 0.7730 (t70) REVERT: R 87 LEU cc_start: 0.8270 (pt) cc_final: 0.8051 (mt) REVERT: R 292 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7597 (t80) REVERT: R 369 MET cc_start: 0.8391 (tpp) cc_final: 0.8102 (tpt) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.1908 time to fit residues: 15.8901 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 : 0.456 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.088027 restraints weight = 9832.539| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.65 r_work: 0.3602 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3823 Z= 0.174 Angle : 0.605 10.672 5207 Z= 0.302 Chirality : 0.039 0.122 585 Planarity : 0.004 0.042 637 Dihedral : 4.285 16.117 491 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.94 % Allowed : 18.27 % Favored : 76.79 % 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: 0.30 (0.40), residues: 443 helix: 0.83 (0.30), residues: 299 sheet: 0.14 (1.91), residues: 12 loop : -1.13 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 399 HIS 0.003 0.001 HIS R 238 PHE 0.010 0.001 PHE E 92 TYR 0.048 0.002 TYR R 46 ARG 0.003 0.000 ARG E 37 *********************** 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 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.427 Fit side-chains REVERT: E 71 ASP cc_start: 0.8622 (m-30) cc_final: 0.7758 (t70) REVERT: R 87 LEU cc_start: 0.8273 (pt) cc_final: 0.8045 (mt) REVERT: R 99 GLU cc_start: 0.7149 (pp20) cc_final: 0.6856 (pp20) REVERT: R 292 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7622 (t80) REVERT: R 373 MET cc_start: 0.8803 (mtm) cc_final: 0.8576 (mtm) outliers start: 20 outliers final: 13 residues processed: 70 average time/residue: 0.1925 time to fit residues: 16.2433 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 : 0.391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.112482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085980 restraints weight = 9828.237| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.67 r_work: 0.3556 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3823 Z= 0.217 Angle : 0.633 9.929 5207 Z= 0.317 Chirality : 0.042 0.144 585 Planarity : 0.004 0.039 637 Dihedral : 4.390 17.048 491 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 0.21 (0.40), residues: 443 helix: 0.80 (0.30), residues: 300 sheet: 0.21 (1.92), residues: 12 loop : -1.32 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 399 HIS 0.004 0.001 HIS R 370 PHE 0.013 0.001 PHE E 44 TYR 0.014 0.002 TYR R 46 ARG 0.003 0.000 ARG E 37 *********************** 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 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.424 Fit side-chains REVERT: E 71 ASP cc_start: 0.8637 (m-30) cc_final: 0.7801 (t70) REVERT: E 76 MET cc_start: 0.8734 (mmm) cc_final: 0.8494 (mmm) REVERT: E 122 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: R 87 LEU cc_start: 0.8260 (pt) cc_final: 0.8012 (mt) REVERT: R 292 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7622 (t80) REVERT: R 373 MET cc_start: 0.8837 (mtm) cc_final: 0.8607 (mtm) outliers start: 18 outliers final: 13 residues processed: 66 average time/residue: 0.1706 time to fit residues: 13.8775 Evaluate side-chains 66 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 347 ILE Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.113338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087312 restraints weight = 9935.350| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.72 r_work: 0.3583 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 3823 Z= 0.202 Angle : 0.653 9.775 5207 Z= 0.327 Chirality : 0.041 0.274 585 Planarity : 0.004 0.041 637 Dihedral : 4.466 17.160 491 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.69 % Allowed : 20.00 % Favored : 75.31 % 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: 0.32 (0.40), residues: 443 helix: 0.86 (0.30), residues: 301 sheet: 0.43 (1.90), residues: 12 loop : -1.21 (0.54), residues: 130 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 E 92 TYR 0.014 0.001 TYR R 46 ARG 0.002 0.000 ARG E 112 *********************** 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 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.464 Fit side-chains REVERT: E 71 ASP cc_start: 0.8600 (m-30) cc_final: 0.7803 (t70) REVERT: E 76 MET cc_start: 0.8716 (mmm) cc_final: 0.8469 (mmm) REVERT: E 122 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: R 87 LEU cc_start: 0.8284 (pt) cc_final: 0.8044 (mt) REVERT: R 230 MET cc_start: 0.8850 (mmm) cc_final: 0.8626 (mmm) REVERT: R 292 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7641 (t80) REVERT: R 373 MET cc_start: 0.8808 (mtm) cc_final: 0.8601 (mtm) outliers start: 19 outliers final: 14 residues processed: 67 average time/residue: 0.1900 time to fit residues: 15.5488 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 : 0.448 ------------------------------------------------------------------------------- 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 130 THR 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 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: 5.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.112478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086587 restraints weight = 9900.272| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.71 r_work: 0.3564 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3823 Z= 0.217 Angle : 0.641 9.412 5207 Z= 0.322 Chirality : 0.041 0.214 585 Planarity : 0.004 0.040 637 Dihedral : 4.473 16.648 491 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 0.32 (0.40), residues: 443 helix: 0.87 (0.30), residues: 299 sheet: 0.49 (1.86), residues: 12 loop : -1.24 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 84 HIS 0.003 0.001 HIS R 370 PHE 0.007 0.001 PHE R 228 TYR 0.013 0.002 TYR E 32 ARG 0.004 0.000 ARG E 64 *********************** 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 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.499 Fit side-chains REVERT: E 48 MET cc_start: 0.8840 (mmm) cc_final: 0.8627 (mmm) REVERT: E 71 ASP cc_start: 0.8578 (m-30) cc_final: 0.7794 (t70) REVERT: E 76 MET cc_start: 0.8721 (mmm) cc_final: 0.8487 (mmm) REVERT: E 122 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: R 87 LEU cc_start: 0.8262 (pt) cc_final: 0.8023 (mt) REVERT: R 230 MET cc_start: 0.8821 (mmm) cc_final: 0.8605 (mmm) REVERT: R 292 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7636 (t80) outliers start: 15 outliers final: 13 residues processed: 64 average time/residue: 0.1649 time to fit residues: 13.2407 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 130 THR 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 344 LEU 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: 6.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0010 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.113566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.087646 restraints weight = 9920.966| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.73 r_work: 0.3590 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3823 Z= 0.189 Angle : 0.629 9.296 5207 Z= 0.314 Chirality : 0.040 0.193 585 Planarity : 0.004 0.042 637 Dihedral : 4.418 18.604 491 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.46 % Allowed : 21.48 % 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: 0.41 (0.40), residues: 443 helix: 0.96 (0.30), residues: 300 sheet: 0.12 (1.80), residues: 12 loop : -1.25 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 84 HIS 0.003 0.001 HIS R 238 PHE 0.006 0.001 PHE R 228 TYR 0.015 0.001 TYR E 32 ARG 0.003 0.000 ARG E 112 ********************** 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 : 0.439 Fit side-chains REVERT: E 48 MET cc_start: 0.8804 (mmm) cc_final: 0.8571 (mmm) REVERT: E 76 MET cc_start: 0.8695 (mmm) cc_final: 0.8475 (mmm) REVERT: E 132 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6092 (mt) REVERT: R 87 LEU cc_start: 0.8318 (pt) cc_final: 0.8065 (mt) REVERT: R 292 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7634 (t80) REVERT: R 373 MET cc_start: 0.8582 (mtm) cc_final: 0.8063 (mtm) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1854 time to fit residues: 14.0359 Evaluate side-chains 62 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 130 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.113087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086931 restraints weight = 9999.602| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.70 r_work: 0.3575 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3823 Z= 0.203 Angle : 0.647 9.371 5207 Z= 0.321 Chirality : 0.040 0.192 585 Planarity : 0.004 0.040 637 Dihedral : 4.411 17.318 491 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.96 % Allowed : 22.47 % Favored : 74.57 % 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: 1.02 (0.30), residues: 299 sheet: 0.09 (1.79), residues: 12 loop : -1.35 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 84 HIS 0.003 0.001 HIS R 370 PHE 0.008 0.001 PHE R 228 TYR 0.016 0.002 TYR E 32 ARG 0.005 0.000 ARG E 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2944.81 seconds wall clock time: 52 minutes 30.92 seconds (3150.92 seconds total)