Starting phenix.real_space_refine on Sat Apr 26 23:14:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj8_36342/04_2025/8jj8_36342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj8_36342/04_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_36342/04_2025/8jj8_36342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj8_36342/04_2025/8jj8_36342.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj8_36342/04_2025/8jj8_36342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj8_36342/04_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-5669/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: 2.84, per 1000 atoms: 0.94 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: 0.85 Conformation dependent library (CDL) restraints added in 365.4 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: 0.23 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: 0.68 Time building geometry restraints manager: 0.98 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: 1.770 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- 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 3093 Z= 0.351 Angle : 0.898 17.416 4200 Z= 0.611 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 Details of bonding type rmsd hydrogen bonds : bond 0.13688 ( 247) hydrogen bonds : angle 5.56686 ( 738) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.50549 ( 4) covalent geometry : bond 0.00530 ( 3091) covalent geometry : angle 0.89806 ( 4196) *********************** 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 : 0.427 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: 0.1275 time to fit residues: 12.4932 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.0370 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.190749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150283 restraints weight = 3693.789| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.63 r_work: 0.3620 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3093 Z= 0.152 Angle : 0.606 5.687 4200 Z= 0.324 Chirality : 0.041 0.157 489 Planarity : 0.003 0.025 515 Dihedral : 9.892 71.790 422 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.86 % Allowed : 7.43 % Favored : 90.71 % 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: 1.01 (0.44), residues: 371 helix: 1.47 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -3.83 (0.71), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 237 HIS 0.002 0.001 HIS F 178 PHE 0.016 0.001 PHE F 284 TYR 0.019 0.002 TYR F 328 ARG 0.006 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 247) hydrogen bonds : angle 4.20168 ( 738) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.52913 ( 4) covalent geometry : bond 0.00323 ( 3091) covalent geometry : angle 0.60651 ( 4196) *********************** 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 69 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.341 Fit side-chains REVERT: F 122 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8081 (mm-30) REVERT: F 230 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6926 (tp) REVERT: F 269 ASP cc_start: 0.7960 (m-30) cc_final: 0.7561 (m-30) REVERT: F 360 ASN cc_start: 0.8101 (t0) cc_final: 0.7734 (m-40) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.1083 time to fit residues: 9.6519 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 : 0.363 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.192580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152724 restraints weight = 3641.555| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.55 r_work: 0.3644 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3093 Z= 0.136 Angle : 0.574 6.641 4200 Z= 0.303 Chirality : 0.039 0.152 489 Planarity : 0.003 0.023 515 Dihedral : 8.762 64.289 415 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.48 % Allowed : 10.22 % Favored : 87.31 % 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: 1.44 (0.44), residues: 371 helix: 1.79 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.64 (0.69), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.015 0.001 PHE F 284 TYR 0.014 0.002 TYR F 324 ARG 0.003 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 247) hydrogen bonds : angle 4.05661 ( 738) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.68725 ( 4) covalent geometry : bond 0.00285 ( 3091) covalent geometry : angle 0.57437 ( 4196) *********************** 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.314 Fit side-chains REVERT: F 122 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7984 (mm-30) REVERT: F 230 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6885 (tp) REVERT: F 243 ASN cc_start: 0.8274 (m-40) cc_final: 0.7800 (m110) REVERT: F 269 ASP cc_start: 0.7971 (m-30) cc_final: 0.7577 (m-30) REVERT: F 360 ASN cc_start: 0.7989 (t0) cc_final: 0.7715 (m-40) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.0886 time to fit residues: 7.6628 Evaluate side-chains 57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.191093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155335 restraints weight = 3758.234| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.44 r_work: 0.3610 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3093 Z= 0.148 Angle : 0.572 6.497 4200 Z= 0.303 Chirality : 0.039 0.127 489 Planarity : 0.003 0.020 515 Dihedral : 8.156 64.503 415 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 12.69 % Favored : 85.14 % 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: 1.48 (0.44), residues: 371 helix: 1.81 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.60 (0.69), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 237 HIS 0.002 0.001 HIS F 363 PHE 0.013 0.001 PHE F 284 TYR 0.024 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 247) hydrogen bonds : angle 4.08545 ( 738) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.08614 ( 4) covalent geometry : bond 0.00326 ( 3091) covalent geometry : angle 0.57168 ( 4196) *********************** 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 59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.340 Fit side-chains REVERT: F 122 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8026 (mm-30) REVERT: F 243 ASN cc_start: 0.8283 (m-40) cc_final: 0.8013 (m110) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.0971 time to fit residues: 7.3429 Evaluate side-chains 59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.189678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153795 restraints weight = 3764.506| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.44 r_work: 0.3593 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3093 Z= 0.150 Angle : 0.566 6.690 4200 Z= 0.300 Chirality : 0.039 0.116 489 Planarity : 0.003 0.019 515 Dihedral : 7.444 65.336 412 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.17 % Allowed : 15.48 % Favored : 82.35 % 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: 1.46 (0.44), residues: 371 helix: 1.80 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.59 (0.67), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.013 0.001 PHE F 284 TYR 0.026 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 247) hydrogen bonds : angle 4.06519 ( 738) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.89729 ( 4) covalent geometry : bond 0.00337 ( 3091) covalent geometry : angle 0.56520 ( 4196) *********************** 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 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.304 Fit side-chains REVERT: F 330 LYS cc_start: 0.6970 (mtpt) cc_final: 0.6695 (ttmt) REVERT: F 342 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5490 (mp) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1013 time to fit residues: 7.5731 Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.187745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151176 restraints weight = 3823.504| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.48 r_work: 0.3574 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3093 Z= 0.174 Angle : 0.595 7.438 4200 Z= 0.317 Chirality : 0.041 0.125 489 Planarity : 0.003 0.019 515 Dihedral : 7.517 66.102 412 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 2.48 % Allowed : 17.34 % Favored : 80.19 % 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: 1.36 (0.44), residues: 371 helix: 1.75 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.48 (0.71), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.015 0.002 PHE F 284 TYR 0.028 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 247) hydrogen bonds : angle 4.12578 ( 738) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.89669 ( 4) covalent geometry : bond 0.00404 ( 3091) covalent geometry : angle 0.59493 ( 4196) *********************** 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 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.332 Fit side-chains REVERT: F 342 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5502 (mp) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1042 time to fit residues: 7.1834 Evaluate side-chains 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.186877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149939 restraints weight = 3784.995| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.49 r_work: 0.3490 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3093 Z= 0.179 Angle : 0.596 7.478 4200 Z= 0.317 Chirality : 0.040 0.124 489 Planarity : 0.003 0.019 515 Dihedral : 7.555 67.249 412 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 17.65 % Favored : 80.19 % 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: 1.28 (0.44), residues: 371 helix: 1.68 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.44 (0.71), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 237 HIS 0.002 0.001 HIS F 172 PHE 0.018 0.002 PHE F 284 TYR 0.024 0.002 TYR F 324 ARG 0.001 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 247) hydrogen bonds : angle 4.15647 ( 738) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.72097 ( 4) covalent geometry : bond 0.00418 ( 3091) covalent geometry : angle 0.59631 ( 4196) *********************** 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 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.314 Fit side-chains REVERT: F 175 ARG cc_start: 0.6855 (mtt90) cc_final: 0.6526 (mpt-90) REVERT: F 251 ASP cc_start: 0.7474 (t0) cc_final: 0.7148 (t0) REVERT: F 342 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5420 (mp) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1277 time to fit residues: 7.9337 Evaluate side-chains 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3326 > 50: distance: 15 - 20: 29.980 distance: 20 - 21: 31.878 distance: 21 - 22: 18.355 distance: 21 - 24: 15.265 distance: 22 - 23: 24.085 distance: 22 - 30: 26.224 distance: 23 - 53: 30.932 distance: 24 - 25: 21.390 distance: 25 - 26: 21.868 distance: 25 - 27: 18.043 distance: 26 - 28: 34.961 distance: 27 - 29: 32.009 distance: 28 - 29: 34.067 distance: 30 - 31: 26.735 distance: 31 - 32: 18.301 distance: 31 - 34: 31.241 distance: 32 - 33: 13.241 distance: 32 - 39: 12.210 distance: 34 - 35: 36.841 distance: 35 - 36: 22.395 distance: 36 - 37: 20.282 distance: 36 - 38: 15.161 distance: 39 - 40: 16.399 distance: 40 - 41: 18.972 distance: 40 - 43: 9.728 distance: 41 - 42: 24.848 distance: 41 - 48: 23.576 distance: 43 - 44: 20.722 distance: 44 - 45: 16.582 distance: 45 - 46: 25.964 distance: 45 - 47: 16.980 distance: 48 - 49: 31.376 distance: 49 - 50: 8.631 distance: 49 - 52: 5.814 distance: 50 - 51: 36.060 distance: 50 - 53: 8.962 distance: 51 - 75: 16.557 distance: 53 - 54: 36.900 distance: 54 - 55: 42.821 distance: 54 - 57: 40.955 distance: 55 - 56: 40.041 distance: 55 - 61: 19.387 distance: 56 - 87: 22.748 distance: 57 - 58: 30.513 distance: 57 - 59: 29.976 distance: 58 - 60: 12.108 distance: 61 - 62: 9.252 distance: 62 - 63: 40.331 distance: 62 - 65: 42.567 distance: 63 - 64: 30.342 distance: 63 - 69: 14.055 distance: 65 - 66: 40.179 distance: 66 - 67: 9.603 distance: 66 - 68: 14.504 distance: 69 - 70: 11.059 distance: 70 - 71: 8.055 distance: 70 - 73: 9.854 distance: 71 - 72: 14.724 distance: 71 - 75: 3.436 distance: 73 - 74: 5.292 distance: 74 - 118: 17.578 distance: 75 - 76: 23.722 distance: 76 - 77: 25.333 distance: 76 - 79: 24.152 distance: 77 - 78: 12.269 distance: 77 - 87: 25.907 distance: 79 - 80: 6.863 distance: 80 - 81: 17.638 distance: 80 - 82: 8.973 distance: 81 - 83: 24.196 distance: 82 - 84: 13.450 distance: 83 - 85: 8.529 distance: 84 - 85: 11.302 distance: 85 - 86: 5.767 distance: 87 - 88: 14.014 distance: 88 - 89: 29.956 distance: 88 - 91: 43.226 distance: 89 - 90: 22.017 distance: 89 - 92: 23.410 distance: 92 - 93: 43.062 distance: 93 - 94: 30.341 distance: 93 - 96: 19.494 distance: 94 - 95: 6.509 distance: 94 - 101: 12.648 distance: 96 - 97: 24.050 distance: 97 - 98: 22.750 distance: 98 - 99: 11.068 distance: 98 - 100: 8.671