Starting phenix.real_space_refine on Tue Mar 3 11:58:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knt_22962/03_2026/7knt_22962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knt_22962/03_2026/7knt_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_22962/03_2026/7knt_22962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knt_22962/03_2026/7knt_22962.map" model { file = "/net/cci-nas-00/data/ceres_data/7knt_22962/03_2026/7knt_22962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knt_22962/03_2026/7knt_22962.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.97, per 1000 atoms: 0.26 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: 0.30 Conformation dependent library (CDL) restraints added in 99.8 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: 0.07 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: 0.60 Time building geometry restraints manager: 0.39 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: 0.610 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG E 112 TYR 0.013 0.001 TYR E 32 PHE 0.011 0.001 PHE E 44 TRP 0.038 0.002 TRP R 399 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3823) covalent geometry : angle 0.75283 ( 5207) SS BOND : bond 0.00352 ( 6) SS BOND : angle 2.31683 ( 12) hydrogen bonds : bond 0.26961 ( 206) hydrogen bonds : angle 8.26399 ( 612) *********************** 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 : 0.150 Fit side-chains revert: symmetry clash REVERT: R 42 MET cc_start: 0.8034 (tpp) cc_final: 0.7806 (tpt) REVERT: R 46 TYR cc_start: 0.7584 (t80) cc_final: 0.7299 (t80) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.0751 time to fit residues: 6.4768 Evaluate side-chains 55 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 86 GLN ** 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 = 0.4174 r_free = 0.4174 target = 0.113988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.087535 restraints weight = 9935.253| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.73 r_work: 0.3589 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3829 Z= 0.149 Angle : 0.682 13.615 5219 Z= 0.351 Chirality : 0.042 0.170 585 Planarity : 0.005 0.043 637 Dihedral : 4.873 29.543 493 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.21 % Allowed : 9.63 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.40), residues: 443 helix: 0.45 (0.30), residues: 290 sheet: -0.65 (1.77), residues: 12 loop : -0.85 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 274 TYR 0.016 0.002 TYR R 46 PHE 0.007 0.001 PHE R 184 TRP 0.021 0.001 TRP R 399 HIS 0.003 0.001 HIS R 238 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3823) covalent geometry : angle 0.67419 ( 5207) SS BOND : bond 0.00352 ( 6) SS BOND : angle 2.25900 ( 12) hydrogen bonds : bond 0.05505 ( 206) hydrogen bonds : angle 5.25671 ( 612) *********************** 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 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.136 Fit side-chains REVERT: E 71 ASP cc_start: 0.8692 (m-30) cc_final: 0.8367 (p0) REVERT: R 46 TYR cc_start: 0.7786 (t80) cc_final: 0.7230 (t80) REVERT: R 292 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7224 (t80) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.0909 time to fit residues: 7.8251 Evaluate side-chains 59 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 292 TYR 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 31 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.113899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.087824 restraints weight = 9798.138| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.69 r_work: 0.3591 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2048 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= 0.142 Angle : 0.663 13.978 5219 Z= 0.327 Chirality : 0.042 0.144 585 Planarity : 0.005 0.040 637 Dihedral : 4.529 16.960 491 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.46 % Allowed : 14.81 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.40), residues: 443 helix: 0.52 (0.30), residues: 300 sheet: -0.39 (1.81), residues: 12 loop : -0.71 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 113 TYR 0.011 0.001 TYR E 32 PHE 0.010 0.001 PHE R 184 TRP 0.019 0.001 TRP R 399 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3823) covalent geometry : angle 0.66038 ( 5207) SS BOND : bond 0.00343 ( 6) SS BOND : angle 1.44229 ( 12) hydrogen bonds : bond 0.04353 ( 206) hydrogen bonds : angle 4.75914 ( 612) *********************** 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 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.093 Fit side-chains REVERT: E 51 VAL cc_start: 0.6717 (OUTLIER) cc_final: 0.6453 (t) REVERT: E 71 ASP cc_start: 0.8634 (m-30) cc_final: 0.8347 (p0) REVERT: R 46 TYR cc_start: 0.7874 (t80) cc_final: 0.7421 (t80) REVERT: R 292 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7487 (t80) REVERT: R 369 MET cc_start: 0.8423 (tpp) cc_final: 0.8180 (tpt) REVERT: R 373 MET cc_start: 0.8994 (mtm) cc_final: 0.8778 (mtm) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.0838 time to fit residues: 6.3975 Evaluate side-chains 65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 153 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 279 ASN ** 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 = 0.4154 r_free = 0.4154 target = 0.113053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.086841 restraints weight = 9728.602| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.66 r_work: 0.3574 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3829 Z= 0.143 Angle : 0.613 12.046 5219 Z= 0.309 Chirality : 0.041 0.119 585 Planarity : 0.004 0.038 637 Dihedral : 4.435 16.763 491 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.20 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.40), residues: 443 helix: 0.72 (0.30), residues: 297 sheet: -0.26 (1.83), residues: 12 loop : -0.98 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 173 TYR 0.011 0.002 TYR R 46 PHE 0.009 0.001 PHE R 184 TRP 0.018 0.001 TRP R 399 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3823) covalent geometry : angle 0.61087 ( 5207) SS BOND : bond 0.00351 ( 6) SS BOND : angle 1.30714 ( 12) hydrogen bonds : bond 0.03801 ( 206) hydrogen bonds : angle 4.48316 ( 612) *********************** 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 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.196 Fit side-chains REVERT: E 51 VAL cc_start: 0.6436 (OUTLIER) cc_final: 0.6186 (t) REVERT: E 71 ASP cc_start: 0.8601 (m-30) cc_final: 0.7626 (t70) REVERT: E 76 MET cc_start: 0.8559 (mmm) cc_final: 0.7850 (mmm) REVERT: R 46 TYR cc_start: 0.7928 (t80) cc_final: 0.7519 (t80) REVERT: R 292 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7534 (t80) REVERT: R 369 MET cc_start: 0.8425 (tpp) cc_final: 0.8158 (tpt) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.1002 time to fit residues: 7.9876 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 51 VAL 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 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 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.111506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084979 restraints weight = 9858.507| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.68 r_work: 0.3537 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2525 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= 0.174 Angle : 0.643 10.055 5219 Z= 0.326 Chirality : 0.042 0.147 585 Planarity : 0.004 0.035 637 Dihedral : 4.501 16.205 491 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.19 % Allowed : 16.79 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.40), residues: 443 helix: 0.58 (0.30), residues: 299 sheet: -0.17 (1.87), residues: 12 loop : -0.99 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 173 TYR 0.011 0.002 TYR R 91 PHE 0.010 0.001 PHE R 308 TRP 0.018 0.001 TRP R 399 HIS 0.005 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3823) covalent geometry : angle 0.64022 ( 5207) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.39495 ( 12) hydrogen bonds : bond 0.03804 ( 206) hydrogen bonds : angle 4.48868 ( 612) *********************** 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 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.144 Fit side-chains REVERT: E 71 ASP cc_start: 0.8672 (m-30) cc_final: 0.7862 (t70) REVERT: R 46 TYR cc_start: 0.8025 (t80) cc_final: 0.7575 (t80) REVERT: R 87 LEU cc_start: 0.8278 (pt) cc_final: 0.8056 (mt) REVERT: R 292 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7633 (t80) REVERT: R 369 MET cc_start: 0.8405 (tpp) cc_final: 0.8183 (tpt) REVERT: R 373 MET cc_start: 0.8936 (mtm) cc_final: 0.8727 (mtm) outliers start: 21 outliers final: 14 residues processed: 70 average time/residue: 0.0752 time to fit residues: 6.4029 Evaluate side-chains 69 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 185 VAL 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 344 LEU 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 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 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 = 0.4157 r_free = 0.4157 target = 0.113209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.086674 restraints weight = 9889.732| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.72 r_work: 0.3578 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3829 Z= 0.128 Angle : 0.607 10.763 5219 Z= 0.305 Chirality : 0.040 0.117 585 Planarity : 0.004 0.039 637 Dihedral : 4.393 14.403 491 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.44 % Allowed : 18.52 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.40), residues: 443 helix: 0.78 (0.30), residues: 300 sheet: -0.10 (1.85), residues: 12 loop : -1.03 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 113 TYR 0.013 0.001 TYR R 91 PHE 0.006 0.001 PHE R 92 TRP 0.024 0.001 TRP E 84 HIS 0.003 0.001 HIS R 238 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3823) covalent geometry : angle 0.60246 ( 5207) SS BOND : bond 0.00635 ( 6) SS BOND : angle 1.70641 ( 12) hydrogen bonds : bond 0.03495 ( 206) hydrogen bonds : angle 4.33848 ( 612) *********************** 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 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.162 Fit side-chains REVERT: E 71 ASP cc_start: 0.8621 (m-30) cc_final: 0.7803 (t70) REVERT: E 122 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: R 87 LEU cc_start: 0.8252 (pt) cc_final: 0.8032 (mt) REVERT: R 292 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7676 (t80) outliers start: 18 outliers final: 11 residues processed: 68 average time/residue: 0.0860 time to fit residues: 7.0392 Evaluate side-chains 65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.0270 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.113727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087351 restraints weight = 9956.729| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.73 r_work: 0.3591 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3829 Z= 0.117 Angle : 0.610 10.215 5219 Z= 0.301 Chirality : 0.040 0.114 585 Planarity : 0.004 0.040 637 Dihedral : 4.332 16.018 491 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.20 % Allowed : 19.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.40), residues: 443 helix: 0.93 (0.30), residues: 298 sheet: 0.21 (1.87), residues: 12 loop : -1.14 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 102 TYR 0.026 0.001 TYR R 46 PHE 0.011 0.001 PHE E 101 TRP 0.026 0.001 TRP E 84 HIS 0.003 0.001 HIS R 238 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3823) covalent geometry : angle 0.60839 ( 5207) SS BOND : bond 0.00629 ( 6) SS BOND : angle 1.05408 ( 12) hydrogen bonds : bond 0.03281 ( 206) hydrogen bonds : angle 4.23252 ( 612) *********************** 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: 17 poor density : 57 time to evaluate : 0.142 Fit side-chains REVERT: E 48 MET cc_start: 0.8934 (mmm) cc_final: 0.8687 (mmt) REVERT: E 71 ASP cc_start: 0.8595 (m-30) cc_final: 0.7759 (t70) REVERT: E 122 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: R 87 LEU cc_start: 0.8278 (pt) cc_final: 0.8051 (mt) REVERT: R 292 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7665 (t80) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.0866 time to fit residues: 6.9688 Evaluate side-chains 64 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0370 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.114711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.088758 restraints weight = 9692.033| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.71 r_work: 0.3619 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3829 Z= 0.126 Angle : 0.652 10.142 5219 Z= 0.326 Chirality : 0.041 0.287 585 Planarity : 0.004 0.042 637 Dihedral : 4.462 21.796 491 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.46 % Allowed : 20.00 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.40), residues: 443 helix: 0.99 (0.30), residues: 298 sheet: 0.27 (1.90), residues: 12 loop : -1.14 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 102 TYR 0.014 0.001 TYR R 46 PHE 0.010 0.001 PHE E 101 TRP 0.026 0.002 TRP E 84 HIS 0.003 0.001 HIS R 238 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3823) covalent geometry : angle 0.63802 ( 5207) SS BOND : bond 0.00502 ( 6) SS BOND : angle 2.87350 ( 12) hydrogen bonds : bond 0.03333 ( 206) hydrogen bonds : angle 4.20691 ( 612) *********************** 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 72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.139 Fit side-chains REVERT: E 48 MET cc_start: 0.8968 (mmm) cc_final: 0.8718 (mmt) REVERT: E 71 ASP cc_start: 0.8572 (m-30) cc_final: 0.7769 (t70) REVERT: E 122 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: E 132 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6058 (mt) REVERT: R 87 LEU cc_start: 0.8232 (pt) cc_final: 0.7992 (mt) REVERT: R 292 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7611 (t80) REVERT: R 373 MET cc_start: 0.8748 (mtm) cc_final: 0.8450 (mtm) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.0626 time to fit residues: 5.2679 Evaluate side-chains 64 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 132 LEU 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 292 TYR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.114183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.088098 restraints weight = 9855.074| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.70 r_work: 0.3605 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3829 Z= 0.129 Angle : 0.695 16.888 5219 Z= 0.332 Chirality : 0.041 0.200 585 Planarity : 0.004 0.040 637 Dihedral : 4.480 19.063 491 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.21 % Allowed : 21.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.40), residues: 443 helix: 1.01 (0.30), residues: 300 sheet: 0.45 (1.86), residues: 12 loop : -1.19 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 37 TYR 0.013 0.001 TYR E 32 PHE 0.009 0.001 PHE E 101 TRP 0.024 0.002 TRP E 84 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3823) covalent geometry : angle 0.68194 ( 5207) SS BOND : bond 0.00419 ( 6) SS BOND : angle 2.88228 ( 12) hydrogen bonds : bond 0.03299 ( 206) hydrogen bonds : angle 4.17986 ( 612) *********************** 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 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.148 Fit side-chains REVERT: E 48 MET cc_start: 0.9031 (mmm) cc_final: 0.8762 (mmt) REVERT: E 122 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: E 132 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6072 (mt) REVERT: R 87 LEU cc_start: 0.8251 (pt) cc_final: 0.8024 (mt) REVERT: R 292 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7632 (t80) REVERT: R 373 MET cc_start: 0.8659 (mtm) cc_final: 0.8245 (mtm) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.0621 time to fit residues: 4.7664 Evaluate side-chains 66 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain R residue 98 SER 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 344 LEU 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 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.088322 restraints weight = 9945.620| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.75 r_work: 0.3608 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3829 Z= 0.127 Angle : 0.681 16.893 5219 Z= 0.329 Chirality : 0.040 0.188 585 Planarity : 0.004 0.041 637 Dihedral : 4.406 17.150 491 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.95 % Allowed : 20.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.40), residues: 443 helix: 1.11 (0.30), residues: 299 sheet: 0.39 (1.82), residues: 12 loop : -1.19 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 112 TYR 0.016 0.001 TYR E 32 PHE 0.015 0.001 PHE R 95 TRP 0.031 0.002 TRP E 84 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3823) covalent geometry : angle 0.67138 ( 5207) SS BOND : bond 0.00416 ( 6) SS BOND : angle 2.43627 ( 12) hydrogen bonds : bond 0.03249 ( 206) hydrogen bonds : angle 4.14182 ( 612) ********************** 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 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.151 Fit side-chains REVERT: E 48 MET cc_start: 0.8968 (mmm) cc_final: 0.8698 (mmt) REVERT: E 76 MET cc_start: 0.8700 (mmm) cc_final: 0.8424 (mmm) REVERT: E 122 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: E 132 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6079 (mt) REVERT: R 87 LEU cc_start: 0.8242 (pt) cc_final: 0.8022 (mt) REVERT: R 292 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7582 (t80) REVERT: R 373 MET cc_start: 0.8773 (mtm) cc_final: 0.8475 (mtm) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.0715 time to fit residues: 5.5426 Evaluate side-chains 68 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 TYR 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 R residue 98 SER 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 344 LEU Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.113651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087325 restraints weight = 9893.487| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.71 r_work: 0.3578 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3295 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= 0.138 Angle : 0.680 16.753 5219 Z= 0.328 Chirality : 0.041 0.180 585 Planarity : 0.004 0.039 637 Dihedral : 4.434 17.125 491 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.21 % Allowed : 21.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.40), residues: 443 helix: 1.02 (0.30), residues: 299 sheet: 0.21 (1.81), residues: 12 loop : -1.24 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 112 TYR 0.017 0.002 TYR E 32 PHE 0.008 0.001 PHE E 101 TRP 0.029 0.002 TRP E 84 HIS 0.004 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3823) covalent geometry : angle 0.67092 ( 5207) SS BOND : bond 0.00461 ( 6) SS BOND : angle 2.36827 ( 12) hydrogen bonds : bond 0.03358 ( 206) hydrogen bonds : angle 4.05845 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.86 seconds wall clock time: 23 minutes 49.12 seconds (1429.12 seconds total)