Starting phenix.real_space_refine on Sun Mar 10 14:42:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/03_2024/8jpf_36478_updated.pdb" } resolution = 3.02 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= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 11 5.16 5 C 1481 2.51 5 N 383 2.21 5 O 393 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 166": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2269 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2178 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.86, per 1000 atoms: 0.82 Number of scatterers: 2269 At special positions: 0 Unit cell: (48.616, 63.448, 83.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 F 1 9.00 O 393 8.00 N 383 7.00 C 1481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 438.3 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 1 sheets defined 77.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'R' and resid 60 through 87 removed outlier: 3.772A pdb=" N VAL R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 126 removed outlier: 3.722A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 171 removed outlier: 3.505A pdb=" N ARG R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 179 Processing helix chain 'R' and resid 182 through 199 Processing helix chain 'R' and resid 201 through 206 Processing helix chain 'R' and resid 230 through 244 Processing helix chain 'R' and resid 246 through 270 Processing helix chain 'R' and resid 294 through 328 removed outlier: 3.991A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 336 through 367 removed outlier: 4.026A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 377 Processing sheet with id= A, first strand: chain 'R' and resid 209 through 211 176 hydrogen bonds defined for protein. 519 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: 0.68 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 372 1.33 - 1.45: 641 1.45 - 1.57: 1295 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2324 Sorted by residual: bond pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 1.329 1.209 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C15 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.348 1.457 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C13 SRW R 501 " pdb=" C16 SRW R 501 " ideal model delta sigma weight residual 1.387 1.290 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.362 1.453 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" CA ARG R 166 " pdb=" C ARG R 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.63e+00 ... (remaining 2319 not shown) Histogram of bond angle deviations from ideal: 56.78 - 72.61: 3 72.61 - 88.43: 0 88.43 - 104.26: 29 104.26 - 120.08: 2137 120.08 - 135.91: 1023 Bond angle restraints: 3192 Sorted by residual: angle pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 71.53 118.99 -47.46 3.00e+00 1.11e-01 2.50e+02 angle pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 162.48 118.92 43.56 3.00e+00 1.11e-01 2.11e+02 angle pdb=" C19 SRW R 501 " pdb=" C18 SRW R 501 " pdb=" N4 SRW R 501 " ideal model delta sigma weight residual 84.97 121.56 -36.59 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C17 SRW R 501 " pdb=" C18 SRW R 501 " pdb=" N4 SRW R 501 " ideal model delta sigma weight residual 154.40 120.08 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N1 SRW R 501 " pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 87.58 119.11 -31.53 3.00e+00 1.11e-01 1.10e+02 ... (remaining 3187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 1248 21.89 - 43.78: 76 43.78 - 65.68: 8 65.68 - 87.57: 2 87.57 - 109.46: 4 Dihedral angle restraints: 1338 sinusoidal: 440 harmonic: 898 Sorted by residual: dihedral pdb=" C8 SRW R 501 " pdb=" C11 SRW R 501 " pdb=" C12 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sinusoidal sigma weight residual 52.96 -56.50 109.46 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C8 SRW R 501 " pdb=" C10 SRW R 501 " pdb=" C9 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sinusoidal sigma weight residual -52.93 49.36 -102.29 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" CA HIS R 132 " pdb=" C HIS R 132 " pdb=" N PRO R 133 " pdb=" CA PRO R 133 " ideal model delta harmonic sigma weight residual 180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.075: 391 1.075 - 2.149: 0 2.149 - 3.224: 0 3.224 - 4.299: 0 4.299 - 5.374: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C8 SRW R 501 " pdb=" C12 SRW R 501 " pdb=" C3 SRW R 501 " pdb=" C9 SRW R 501 " both_signs ideal model delta sigma weight residual False 2.71 -2.66 5.37 2.00e-01 2.50e+01 7.22e+02 chirality pdb=" CA VAL R 56 " pdb=" N VAL R 56 " pdb=" C VAL R 56 " pdb=" CB VAL R 56 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL R 223 " pdb=" N VAL R 223 " pdb=" C VAL R 223 " pdb=" CB VAL R 223 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 389 not shown) Planarity restraints: 391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 132 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO R 133 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 133 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 133 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 165 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.11e+00 pdb=" C GLU R 165 " -0.018 2.00e-02 2.50e+03 pdb=" O GLU R 165 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG R 166 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 166 " 0.004 2.00e-02 2.50e+03 8.62e-03 7.43e-01 pdb=" C ARG R 166 " -0.015 2.00e-02 2.50e+03 pdb=" O ARG R 166 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR R 167 " 0.005 2.00e-02 2.50e+03 ... (remaining 388 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 331 2.75 - 3.29: 2438 3.29 - 3.83: 4003 3.83 - 4.36: 4232 4.36 - 4.90: 7704 Nonbonded interactions: 18708 Sorted by model distance: nonbonded pdb=" OE1 GLU R 123 " pdb=" OH TYR R 354 " model vdw 2.214 2.440 nonbonded pdb=" OD2 ASP R 112 " pdb=" ND2 ASN R 360 " model vdw 2.347 2.520 nonbonded pdb=" OH TYR L 11 " pdb=" O LEU R 54 " model vdw 2.352 2.440 nonbonded pdb=" O GLU R 123 " pdb=" N ILE R 128 " model vdw 2.410 2.520 nonbonded pdb=" OD1 ASP R 138 " pdb=" N ALA R 139 " model vdw 2.414 2.520 ... (remaining 18703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 6.580 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.460 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.006 0.120 2324 Z= 0.414 Angle : 1.757 47.456 3192 Z= 0.646 Chirality : 0.274 5.374 392 Planarity : 0.004 0.037 391 Dihedral : 15.609 109.459 754 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 7.34 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.48), residues: 296 helix: 2.15 (0.32), residues: 232 sheet: None (None), residues: 0 loop : -1.00 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 134 HIS 0.003 0.001 HIS R 343 PHE 0.012 0.001 PHE R 375 TYR 0.014 0.002 TYR R 319 ARG 0.004 0.000 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.249 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2218 time to fit residues: 10.5945 Evaluate side-chains 36 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2324 Z= 0.193 Angle : 0.603 6.712 3192 Z= 0.300 Chirality : 0.040 0.146 392 Planarity : 0.004 0.033 391 Dihedral : 7.060 63.648 340 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 7.80 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.48), residues: 296 helix: 2.16 (0.32), residues: 231 sheet: -3.87 (1.03), residues: 10 loop : -0.56 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 134 HIS 0.004 0.001 HIS R 343 PHE 0.016 0.002 PHE R 375 TYR 0.016 0.002 TYR R 364 ARG 0.003 0.001 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: R 364 TYR cc_start: 0.7850 (m-80) cc_final: 0.7544 (m-80) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1806 time to fit residues: 9.7920 Evaluate side-chains 45 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 14 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 158 ASN R 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.196 Angle : 0.589 7.197 3192 Z= 0.292 Chirality : 0.040 0.129 392 Planarity : 0.004 0.036 391 Dihedral : 8.282 68.755 340 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.83 % Allowed : 11.01 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.48), residues: 296 helix: 2.08 (0.32), residues: 234 sheet: -3.35 (1.19), residues: 10 loop : -0.72 (0.91), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 375 TYR 0.014 0.002 TYR R 319 ARG 0.002 0.000 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 262 LYS cc_start: 0.7987 (tptt) cc_final: 0.7741 (tptm) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1853 time to fit residues: 9.4222 Evaluate side-chains 43 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.206 Angle : 0.581 6.733 3192 Z= 0.292 Chirality : 0.040 0.123 392 Planarity : 0.004 0.037 391 Dihedral : 8.797 70.489 340 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.29 % Allowed : 11.01 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.48), residues: 296 helix: 2.04 (0.32), residues: 229 sheet: -3.15 (1.35), residues: 10 loop : -0.72 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.016 0.002 PHE R 375 TYR 0.019 0.002 TYR R 364 ARG 0.002 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.232 Fit side-chains REVERT: R 262 LYS cc_start: 0.8006 (tptt) cc_final: 0.7760 (tptm) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1805 time to fit residues: 9.1975 Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2324 Z= 0.307 Angle : 0.643 6.725 3192 Z= 0.327 Chirality : 0.043 0.146 392 Planarity : 0.004 0.038 391 Dihedral : 9.358 77.509 340 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.67 % Allowed : 10.55 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.47), residues: 296 helix: 1.83 (0.32), residues: 228 sheet: -2.90 (1.53), residues: 10 loop : -0.95 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.019 0.002 PHE R 205 TYR 0.023 0.003 TYR R 364 ARG 0.005 0.001 ARG R 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.262 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.1678 time to fit residues: 8.6306 Evaluate side-chains 47 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 306 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2324 Z= 0.193 Angle : 0.568 6.823 3192 Z= 0.292 Chirality : 0.040 0.127 392 Planarity : 0.004 0.038 391 Dihedral : 9.528 88.904 340 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 12.39 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.48), residues: 296 helix: 1.92 (0.33), residues: 228 sheet: -2.56 (1.66), residues: 10 loop : -0.87 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.016 0.002 PHE R 205 TYR 0.023 0.002 TYR R 364 ARG 0.002 0.000 ARG R 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.240 Fit side-chains REVERT: R 262 LYS cc_start: 0.7989 (tptt) cc_final: 0.7742 (tptm) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.1610 time to fit residues: 8.0734 Evaluate side-chains 43 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.204 Angle : 0.576 6.633 3192 Z= 0.297 Chirality : 0.040 0.128 392 Planarity : 0.004 0.038 391 Dihedral : 9.844 95.888 340 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 14.68 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.48), residues: 296 helix: 1.95 (0.32), residues: 227 sheet: -2.19 (1.75), residues: 10 loop : -0.91 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 205 TYR 0.025 0.002 TYR R 364 ARG 0.002 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.265 Fit side-chains REVERT: R 262 LYS cc_start: 0.7947 (tptt) cc_final: 0.7713 (tptm) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1740 time to fit residues: 8.9210 Evaluate side-chains 45 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2324 Z= 0.208 Angle : 0.585 6.947 3192 Z= 0.300 Chirality : 0.040 0.125 392 Planarity : 0.004 0.038 391 Dihedral : 10.086 100.602 340 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.21 % Allowed : 15.14 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.48), residues: 296 helix: 1.95 (0.32), residues: 227 sheet: -1.93 (1.85), residues: 10 loop : -1.06 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 205 TYR 0.025 0.002 TYR R 364 ARG 0.005 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.268 Fit side-chains REVERT: R 262 LYS cc_start: 0.7948 (tptt) cc_final: 0.7716 (tptm) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1722 time to fit residues: 8.8428 Evaluate side-chains 46 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2324 Z= 0.188 Angle : 0.602 12.407 3192 Z= 0.301 Chirality : 0.039 0.126 392 Planarity : 0.004 0.038 391 Dihedral : 9.948 100.013 340 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 16.06 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.48), residues: 296 helix: 2.00 (0.32), residues: 227 sheet: -1.72 (1.91), residues: 10 loop : -1.01 (0.81), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.015 0.001 PHE R 205 TYR 0.027 0.002 TYR R 364 ARG 0.003 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: R 262 LYS cc_start: 0.7914 (tptt) cc_final: 0.7706 (tptm) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.1675 time to fit residues: 8.7940 Evaluate side-chains 45 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2324 Z= 0.198 Angle : 0.608 11.948 3192 Z= 0.308 Chirality : 0.040 0.132 392 Planarity : 0.004 0.038 391 Dihedral : 9.996 101.160 340 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 16.97 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.48), residues: 296 helix: 1.99 (0.32), residues: 228 sheet: -1.49 (2.03), residues: 10 loop : -1.20 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.002 0.001 HIS R 343 PHE 0.014 0.001 PHE R 205 TYR 0.026 0.003 TYR R 364 ARG 0.003 0.000 ARG L 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.278 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.1650 time to fit residues: 8.6861 Evaluate side-chains 46 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148880 restraints weight = 3560.786| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.17 r_work: 0.3748 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2324 Z= 0.197 Angle : 0.629 12.074 3192 Z= 0.314 Chirality : 0.040 0.131 392 Planarity : 0.004 0.038 391 Dihedral : 9.978 101.370 340 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.75 % Allowed : 15.60 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.48), residues: 296 helix: 1.95 (0.32), residues: 228 sheet: -1.35 (2.10), residues: 10 loop : -1.17 (0.83), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.002 0.001 HIS R 343 PHE 0.014 0.001 PHE R 205 TYR 0.026 0.003 TYR R 364 ARG 0.003 0.000 ARG L 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 998.31 seconds wall clock time: 19 minutes 21.61 seconds (1161.61 seconds total)