Starting phenix.real_space_refine on Wed Mar 5 21:45:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj8_36342/03_2025/8jj8_36342.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic. 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 20 5.16 5 C 1984 2.51 5 N 488 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3023 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.64, per 1000 atoms: 0.87 Number of scatterers: 3023 At special positions: 0 Unit cell: (57.78, 103.79, 82.39, 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 20 16.00 O 531 8.00 N 488 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 106 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 190 " 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: 0.74 Conformation dependent library (CDL) restraints added in 327.9 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'F' and resid 30 through 56 removed outlier: 4.023A pdb=" N MET F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 93 removed outlier: 3.531A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 102 through 136 Processing helix chain 'F' and resid 137 through 143 removed outlier: 4.230A pdb=" N SER F 143 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.261A pdb=" N MET F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 removed outlier: 3.780A pdb=" N ASN F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 Processing helix chain 'F' and resid 208 through 249 removed outlier: 3.608A pdb=" N LYS F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 273 removed outlier: 3.682A pdb=" N VAL F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 305 Processing helix chain 'F' and resid 306 through 365 removed outlier: 4.741A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.920A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.517A pdb=" N ILE F 370 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 384 Processing helix chain 'F' and resid 384 through 389 removed outlier: 3.606A pdb=" N PHE F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 396 through 407 removed outlier: 3.590A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 738 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: 0.79 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 478 1.29 - 1.42: 820 1.42 - 1.55: 1760 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 3091 Sorted by residual: bond pdb=" C TYR F 328 " pdb=" O TYR F 328 " ideal model delta sigma weight residual 1.236 1.161 0.076 1.26e-02 6.30e+03 3.61e+01 bond pdb=" C LYS F 327 " pdb=" O LYS F 327 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.61e+01 bond pdb=" C GLN F 326 " pdb=" O GLN F 326 " ideal model delta sigma weight residual 1.235 1.286 -0.050 1.26e-02 6.30e+03 1.60e+01 bond pdb=" C LEU F 342 " pdb=" O LEU F 342 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.26e-02 6.30e+03 1.27e+01 bond pdb=" C ALA F 338 " pdb=" O ALA F 338 " ideal model delta sigma weight residual 1.236 1.281 -0.045 1.29e-02 6.01e+03 1.22e+01 ... (remaining 3086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 4144 3.48 - 6.97: 46 6.97 - 10.45: 5 10.45 - 13.93: 0 13.93 - 17.42: 1 Bond angle restraints: 4196 Sorted by residual: angle pdb=" O ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 121.96 130.61 -8.65 8.40e-01 1.42e+00 1.06e+02 angle pdb=" CA ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 115.25 106.83 8.42 9.50e-01 1.11e+00 7.85e+01 angle pdb=" N LYS F 340 " pdb=" CA LYS F 340 " pdb=" C LYS F 340 " ideal model delta sigma weight residual 111.28 102.34 8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N GLN F 326 " pdb=" CA GLN F 326 " pdb=" C GLN F 326 " ideal model delta sigma weight residual 110.80 93.38 17.42 2.13e+00 2.20e-01 6.69e+01 angle pdb=" N LEU F 329 " pdb=" CA LEU F 329 " pdb=" C LEU F 329 " ideal model delta sigma weight residual 111.07 103.97 7.10 1.07e+00 8.73e-01 4.41e+01 ... (remaining 4191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1615 17.82 - 35.64: 168 35.64 - 53.46: 33 53.46 - 71.28: 4 71.28 - 89.10: 6 Dihedral angle restraints: 1826 sinusoidal: 718 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 106 " pdb=" SG CYS F 106 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CA MET F 96 " pdb=" C MET F 96 " pdb=" N LYS F 97 " pdb=" CA LYS F 97 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CA GLN F 326 " pdb=" CB GLN F 326 " ideal model delta harmonic sigma weight residual 122.80 114.83 7.97 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 1823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 399 0.060 - 0.120: 80 0.120 - 0.180: 6 0.180 - 0.240: 2 0.240 - 0.300: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA GLN F 326 " pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CB GLN F 326 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LEU F 339 " pdb=" N LEU F 339 " pdb=" C LEU F 339 " pdb=" CB LEU F 339 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 486 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 326 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLN F 326 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN F 326 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS F 327 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 329 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU F 329 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU F 329 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS F 330 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 236 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C ASN F 236 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN F 236 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP F 237 " 0.016 2.00e-02 2.50e+03 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 57 2.67 - 3.22: 3111 3.22 - 3.78: 4782 3.78 - 4.34: 6157 4.34 - 4.90: 10166 Nonbonded interactions: 24273 Sorted by model distance: nonbonded pdb=" OE2 GLU F 187 " pdb=" OG1 THR F 189 " model vdw 2.107 3.040 nonbonded pdb=" OG SER F 203 " pdb=" O2 H98 F 501 " model vdw 2.191 3.040 nonbonded pdb=" O THR F 341 " pdb=" C LEU F 342 " model vdw 2.229 3.270 nonbonded pdb=" O THR F 239 " pdb=" ND2 ASN F 243 " model vdw 2.315 3.120 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.323 3.040 ... (remaining 24268 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.005 0.076 3091 Z= 0.343 Angle : 0.898 17.416 4196 Z= 0.612 Chirality : 0.050 0.300 489 Planarity : 0.005 0.042 515 Dihedral : 15.213 81.138 1098 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.86 % Allowed : 1.55 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.45), residues: 371 helix: 1.06 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -3.25 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.021 0.002 PHE F 284 TYR 0.020 0.002 TYR F 328 ARG 0.007 0.001 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.330 Fit side-chains REVERT: F 230 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7669 (tp) REVERT: F 269 ASP cc_start: 0.7008 (m-30) cc_final: 0.6792 (m-30) REVERT: F 331 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (t80) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.1248 time to fit residues: 12.1918 Evaluate side-chains 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN F 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.190209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149065 restraints weight = 3699.490| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.66 r_work: 0.3600 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3091 Z= 0.234 Angle : 0.610 5.582 4196 Z= 0.326 Chirality : 0.042 0.160 489 Planarity : 0.003 0.024 515 Dihedral : 9.805 69.586 422 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 6.81 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.44), residues: 371 helix: 1.47 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.70 (0.70), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 237 HIS 0.002 0.000 HIS F 178 PHE 0.016 0.001 PHE F 284 TYR 0.021 0.002 TYR F 328 ARG 0.006 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.303 Fit side-chains REVERT: F 122 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8117 (mm-30) REVERT: F 230 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6859 (tp) REVERT: F 269 ASP cc_start: 0.7962 (m-30) cc_final: 0.7580 (m-30) REVERT: F 326 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7962 (mm-40) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.0998 time to fit residues: 9.0247 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.190326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150180 restraints weight = 3663.200| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.54 r_work: 0.3604 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3091 Z= 0.232 Angle : 0.591 6.733 4196 Z= 0.313 Chirality : 0.040 0.148 489 Planarity : 0.003 0.023 515 Dihedral : 8.850 64.975 415 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.48 % Allowed : 10.84 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.27 (0.44), residues: 371 helix: 1.67 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.66 (0.68), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.015 0.002 PHE F 284 TYR 0.014 0.002 TYR F 324 ARG 0.003 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.334 Fit side-chains REVERT: F 122 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7992 (mm-30) REVERT: F 230 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6931 (tp) REVERT: F 269 ASP cc_start: 0.7986 (m-30) cc_final: 0.7617 (m-30) REVERT: F 326 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7821 (mm-40) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 0.0926 time to fit residues: 7.3299 Evaluate side-chains 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.189654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153339 restraints weight = 3767.592| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.44 r_work: 0.3587 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3091 Z= 0.234 Angle : 0.578 6.872 4196 Z= 0.307 Chirality : 0.040 0.131 489 Planarity : 0.003 0.019 515 Dihedral : 8.142 65.958 415 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.17 % Allowed : 13.31 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.34 (0.44), residues: 371 helix: 1.72 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.64 (0.67), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 237 HIS 0.002 0.001 HIS F 178 PHE 0.013 0.002 PHE F 284 TYR 0.015 0.002 TYR F 324 ARG 0.003 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.342 Fit side-chains REVERT: F 122 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8013 (mm-30) REVERT: F 326 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7824 (mm-40) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1050 time to fit residues: 7.3821 Evaluate side-chains 53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.191840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155868 restraints weight = 3741.110| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.46 r_work: 0.3626 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3091 Z= 0.185 Angle : 0.540 6.615 4196 Z= 0.287 Chirality : 0.038 0.111 489 Planarity : 0.003 0.020 515 Dihedral : 7.353 65.124 412 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 14.86 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.56 (0.45), residues: 371 helix: 1.91 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -3.73 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.015 0.001 PHE F 284 TYR 0.018 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.309 Fit side-chains REVERT: F 243 ASN cc_start: 0.8188 (m-40) cc_final: 0.7748 (m110) REVERT: F 342 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.5749 (mp) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0965 time to fit residues: 7.5208 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.189864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153497 restraints weight = 3825.924| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.48 r_work: 0.3584 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3091 Z= 0.233 Angle : 0.576 7.586 4196 Z= 0.307 Chirality : 0.039 0.118 489 Planarity : 0.003 0.024 515 Dihedral : 7.396 65.375 412 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.48 % Allowed : 17.65 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.54 (0.45), residues: 371 helix: 1.89 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.53 (0.71), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.015 0.001 PHE F 284 TYR 0.019 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.321 Fit side-chains REVERT: F 243 ASN cc_start: 0.8193 (m-40) cc_final: 0.7870 (m110) REVERT: F 251 ASP cc_start: 0.7609 (t0) cc_final: 0.7309 (t0) REVERT: F 342 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.5662 (mp) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.0902 time to fit residues: 6.6951 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151129 restraints weight = 3745.914| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.62 r_work: 0.3627 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3091 Z= 0.191 Angle : 0.557 7.551 4196 Z= 0.296 Chirality : 0.039 0.126 489 Planarity : 0.003 0.019 515 Dihedral : 7.289 64.967 412 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.17 % Allowed : 17.96 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.67 (0.45), residues: 371 helix: 1.97 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.40 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.016 0.001 PHE F 284 TYR 0.024 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.317 Fit side-chains REVERT: F 99 TRP cc_start: 0.8165 (t-100) cc_final: 0.7714 (t-100) REVERT: F 243 ASN cc_start: 0.8161 (m-40) cc_final: 0.7738 (m110) REVERT: F 251 ASP cc_start: 0.7570 (t0) cc_final: 0.7273 (t0) REVERT: F 342 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.5633 (mp) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.0956 time to fit residues: 6.8148 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150836 restraints weight = 3763.133| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.62 r_work: 0.3626 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3091 Z= 0.194 Angle : 0.564 7.934 4196 Z= 0.300 Chirality : 0.039 0.119 489 Planarity : 0.003 0.019 515 Dihedral : 7.243 64.395 412 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.55 % Allowed : 19.20 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.73 (0.45), residues: 371 helix: 2.01 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.36 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.017 0.001 PHE F 284 TYR 0.025 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.308 Fit side-chains REVERT: F 243 ASN cc_start: 0.8107 (m-40) cc_final: 0.7790 (m110) REVERT: F 251 ASP cc_start: 0.7537 (t0) cc_final: 0.7327 (t0) REVERT: F 269 ASP cc_start: 0.7966 (m-30) cc_final: 0.7618 (m-30) REVERT: F 342 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5716 (mp) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.0880 time to fit residues: 6.4628 Evaluate side-chains 50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145572 restraints weight = 3793.353| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.74 r_work: 0.3612 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3091 Z= 0.189 Angle : 0.565 8.067 4196 Z= 0.300 Chirality : 0.039 0.123 489 Planarity : 0.003 0.019 515 Dihedral : 7.233 63.780 412 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.55 % Allowed : 18.58 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.87 (0.45), residues: 371 helix: 2.08 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -3.20 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.018 0.001 PHE F 284 TYR 0.024 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.336 Fit side-chains REVERT: F 243 ASN cc_start: 0.8091 (m-40) cc_final: 0.7787 (m110) REVERT: F 269 ASP cc_start: 0.7947 (m-30) cc_final: 0.7566 (m-30) REVERT: F 342 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.5806 (mp) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.0933 time to fit residues: 6.5763 Evaluate side-chains 49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.191188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149920 restraints weight = 3661.281| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.65 r_work: 0.3621 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3091 Z= 0.195 Angle : 0.594 8.353 4196 Z= 0.310 Chirality : 0.039 0.125 489 Planarity : 0.003 0.019 515 Dihedral : 7.210 63.576 412 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.55 % Allowed : 20.12 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.88 (0.46), residues: 371 helix: 2.08 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -3.16 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.018 0.001 PHE F 284 TYR 0.024 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.351 Fit side-chains REVERT: F 122 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8340 (mm-30) REVERT: F 130 ASP cc_start: 0.8649 (t70) cc_final: 0.8004 (t0) REVERT: F 243 ASN cc_start: 0.8081 (m-40) cc_final: 0.7773 (m110) REVERT: F 269 ASP cc_start: 0.7958 (m-30) cc_final: 0.7578 (m-30) REVERT: F 342 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.5919 (mp) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1008 time to fit residues: 6.6988 Evaluate side-chains 48 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.191593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150856 restraints weight = 3686.804| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.65 r_work: 0.3618 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3091 Z= 0.188 Angle : 0.585 8.224 4196 Z= 0.305 Chirality : 0.039 0.124 489 Planarity : 0.003 0.019 515 Dihedral : 7.173 63.321 412 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.24 % Allowed : 20.43 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.46), residues: 371 helix: 2.10 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -3.07 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.017 0.001 PHE F 284 TYR 0.022 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1819.87 seconds wall clock time: 32 minutes 1.21 seconds (1921.21 seconds total)