Starting phenix.real_space_refine on Tue Mar 3 11:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkh_14042/03_2026/7qkh_14042.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 945 2.51 5 N 273 2.21 5 O 288 1.98 5 H 1593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "B" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "D" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 0.73, per 1000 atoms: 0.24 Number of scatterers: 3105 At special positions: 0 Unit cell: (58.16, 139.584, 33.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 288 8.00 N 273 7.00 C 945 6.00 H 1593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.26 Conformation dependent library (CDL) restraints added in 84.7 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA2, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA3, first strand: chain 'B' and resid 296 through 297 removed outlier: 6.313A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 305 through 309 removed outlier: 6.260A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.460A pdb=" N LYS G 294 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 298 through 299 removed outlier: 6.582A pdb=" N LYS G 298 " --> pdb=" O HIS E 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.383A pdb=" N VAL G 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 316 32 hydrogen bonds defined for protein. 96 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: 0.55 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 1586 1.09 - 1.27: 256 1.27 - 1.45: 348 1.45 - 1.63: 924 1.63 - 1.81: 6 Bond restraints: 3120 Sorted by residual: bond pdb=" N ILE A 297 " pdb=" H ILE A 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE G 297 " pdb=" H ILE G 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS B 298 " pdb=" H LYS B 298 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N HIS D 299 " pdb=" H HIS D 299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NE2 GLN B 307 " pdb="HE21 GLN B 307 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.40: 5614 7.40 - 14.80: 48 14.80 - 22.21: 7 22.21 - 29.61: 9 29.61 - 37.01: 13 Bond angle restraints: 5691 Sorted by residual: angle pdb=" CB VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 109.00 71.99 37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA VAL E 313 " pdb=" CB VAL E 313 " pdb=" HB VAL E 313 " ideal model delta sigma weight residual 109.00 72.93 36.07 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" HA VAL G 313 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 110.00 74.59 35.41 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" HA VAL C 313 " ideal model delta sigma weight residual 110.00 75.23 34.77 3.00e+00 1.11e-01 1.34e+02 ... (remaining 5686 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.34: 1193 15.34 - 30.66: 151 30.66 - 45.99: 31 45.99 - 61.32: 43 61.32 - 76.65: 25 Dihedral angle restraints: 1443 sinusoidal: 837 harmonic: 606 Sorted by residual: dihedral pdb=" C VAL C 313 " pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual -122.00 -141.49 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" C VAL G 313 " pdb=" N VAL G 313 " pdb=" CA VAL G 313 " pdb=" CB VAL G 313 " ideal model delta harmonic sigma weight residual -122.00 -139.63 17.63 0 2.50e+00 1.60e-01 4.97e+01 dihedral pdb=" N VAL C 313 " pdb=" C VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual 123.40 140.78 -17.38 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 222 0.248 - 0.495: 8 0.495 - 0.743: 3 0.743 - 0.990: 3 0.990 - 1.238: 1 Chirality restraints: 237 Sorted by residual: chirality pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" CG1 VAL G 313 " pdb=" CG2 VAL G 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL G 287 " pdb=" CA VAL G 287 " pdb=" CG1 VAL G 287 " pdb=" CG2 VAL G 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.65 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 234 not shown) Planarity restraints: 447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 286 " -0.024 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG ASN B 286 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 286 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN B 286 " 0.171 2.00e-02 2.50e+03 pdb="HD21 ASN B 286 " -0.080 2.00e-02 2.50e+03 pdb="HD22 ASN B 286 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.116 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 286 " -0.043 2.00e-02 2.50e+03 6.96e-02 7.27e+01 pdb=" CG ASN A 286 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 286 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 286 " 0.134 2.00e-02 2.50e+03 pdb="HD21 ASN A 286 " -0.020 2.00e-02 2.50e+03 pdb="HD22 ASN A 286 " -0.093 2.00e-02 2.50e+03 ... (remaining 444 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 396 2.26 - 2.84: 6035 2.84 - 3.43: 8037 3.43 - 4.01: 10197 4.01 - 4.60: 14619 Nonbonded interactions: 39284 Sorted by model distance: nonbonded pdb=" H VAL C 313 " pdb=" HA VAL C 313 " model vdw 1.669 1.816 nonbonded pdb=" HZ3 LYS G 294 " pdb=" OD2 ASP B 295 " model vdw 1.697 2.450 nonbonded pdb=" H VAL E 313 " pdb=" HA VAL E 313 " model vdw 1.701 1.816 nonbonded pdb="HG21 ILE B 277 " pdb=" H ILE B 278 " model vdw 1.719 2.270 nonbonded pdb=" H VAL G 313 " pdb=" HA VAL G 313 " model vdw 1.720 1.816 ... (remaining 39279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.011 0.039 1527 Z= 0.705 Angle : 2.478 18.649 2043 Z= 1.587 Chirality : 0.194 1.238 237 Planarity : 0.012 0.062 258 Dihedral : 15.219 74.648 585 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 2.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.42), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.32), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.109 0.031 TYR A 310 HIS 0.010 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.01134 ( 1527) covalent geometry : angle 2.47810 ( 2043) hydrogen bonds : bond 0.08934 ( 28) hydrogen bonds : angle 7.10654 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: C 290 LYS cc_start: 0.7766 (pttt) cc_final: 0.5963 (mmtm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1745 time to fit residues: 5.9116 Evaluate side-chains 18 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.130934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.119536 restraints weight = 7379.082| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.23 r_work: 0.4280 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4199 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1527 Z= 0.170 Angle : 1.075 11.681 2043 Z= 0.565 Chirality : 0.218 1.497 237 Planarity : 0.003 0.020 258 Dihedral : 9.134 23.945 204 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.56 % Allowed : 16.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.43), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.33), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 310 HIS 0.005 0.002 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 1527) covalent geometry : angle 1.07532 ( 2043) hydrogen bonds : bond 0.02193 ( 28) hydrogen bonds : angle 5.32395 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.086 Fit side-chains REVERT: G 305 SER cc_start: 0.8306 (p) cc_final: 0.7891 (m) REVERT: C 290 LYS cc_start: 0.8037 (pttt) cc_final: 0.5413 (mmtm) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1082 time to fit residues: 2.5265 Evaluate side-chains 16 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.132307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.120648 restraints weight = 7314.265| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.22 r_work: 0.4286 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4205 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1527 Z= 0.132 Angle : 0.988 11.221 2043 Z= 0.521 Chirality : 0.219 1.471 237 Planarity : 0.003 0.025 258 Dihedral : 7.958 20.308 204 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 310 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 1527) covalent geometry : angle 0.98771 ( 2043) hydrogen bonds : bond 0.02546 ( 28) hydrogen bonds : angle 4.65087 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.055 Fit side-chains REVERT: A 308 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7535 (mt) REVERT: G 290 LYS cc_start: 0.7768 (pttt) cc_final: 0.7503 (ptpp) REVERT: B 290 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7213 (tptt) REVERT: B 308 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7052 (mt) REVERT: C 290 LYS cc_start: 0.7893 (pttt) cc_final: 0.5208 (mmmt) REVERT: E 305 SER cc_start: 0.8266 (p) cc_final: 0.7811 (m) outliers start: 4 outliers final: 1 residues processed: 21 average time/residue: 0.1412 time to fit residues: 3.3726 Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.135005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.123156 restraints weight = 7239.868| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.24 r_work: 0.4322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1527 Z= 0.116 Angle : 0.934 11.101 2043 Z= 0.492 Chirality : 0.218 1.460 237 Planarity : 0.004 0.031 258 Dihedral : 6.942 19.117 204 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR E 310 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 1527) covalent geometry : angle 0.93422 ( 2043) hydrogen bonds : bond 0.01953 ( 28) hydrogen bonds : angle 4.32539 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: G 290 LYS cc_start: 0.7752 (pttt) cc_final: 0.7309 (ptpp) REVERT: B 290 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7208 (tptt) REVERT: B 308 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7221 (mt) REVERT: D 309 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8073 (p) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.1146 time to fit residues: 2.7130 Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.137844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.125747 restraints weight = 7200.493| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.31 r_work: 0.4340 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1527 Z= 0.108 Angle : 0.907 11.165 2043 Z= 0.477 Chirality : 0.218 1.475 237 Planarity : 0.004 0.036 258 Dihedral : 6.332 18.464 204 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.11 % Allowed : 17.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 1527) covalent geometry : angle 0.90689 ( 2043) hydrogen bonds : bond 0.01782 ( 28) hydrogen bonds : angle 4.07315 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.1079 time to fit residues: 2.2447 Evaluate side-chains 19 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.125481 restraints weight = 7230.091| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.31 r_work: 0.4349 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4268 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1527 Z= 0.109 Angle : 0.905 11.152 2043 Z= 0.474 Chirality : 0.218 1.474 237 Planarity : 0.004 0.035 258 Dihedral : 6.054 17.494 204 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.67 % Allowed : 17.22 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR E 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 1527) covalent geometry : angle 0.90467 ( 2043) hydrogen bonds : bond 0.01770 ( 28) hydrogen bonds : angle 3.88235 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: E 310 TYR cc_start: 0.8260 (t80) cc_final: 0.7617 (t80) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.0861 time to fit residues: 1.9528 Evaluate side-chains 19 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.140183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.128093 restraints weight = 7259.063| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.31 r_work: 0.4359 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4277 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.107 Angle : 0.891 11.145 2043 Z= 0.468 Chirality : 0.219 1.475 237 Planarity : 0.004 0.036 258 Dihedral : 5.615 16.350 204 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 16.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR E 310 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 1527) covalent geometry : angle 0.89139 ( 2043) hydrogen bonds : bond 0.01656 ( 28) hydrogen bonds : angle 3.71072 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: B 308 ILE cc_start: 0.7472 (tt) cc_final: 0.7160 (mt) REVERT: E 310 TYR cc_start: 0.8284 (t80) cc_final: 0.7629 (t80) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1147 time to fit residues: 2.3298 Evaluate side-chains 19 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4509 r_free = 0.4509 target = 0.137592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.125587 restraints weight = 7409.151| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.28 r_work: 0.4332 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4251 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.113 Angle : 0.893 11.241 2043 Z= 0.468 Chirality : 0.218 1.478 237 Planarity : 0.004 0.035 258 Dihedral : 5.723 16.065 204 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 16.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 310 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 1527) covalent geometry : angle 0.89336 ( 2043) hydrogen bonds : bond 0.01629 ( 28) hydrogen bonds : angle 3.55643 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 308 ILE cc_start: 0.7507 (tt) cc_final: 0.7209 (mt) REVERT: E 310 TYR cc_start: 0.8274 (t80) cc_final: 0.7710 (t80) outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0982 time to fit residues: 2.2478 Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.140212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.128086 restraints weight = 7243.195| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.31 r_work: 0.4368 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4287 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.103 Angle : 0.879 11.065 2043 Z= 0.461 Chirality : 0.217 1.466 237 Planarity : 0.004 0.034 258 Dihedral : 5.340 15.708 204 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 16.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR E 310 HIS 0.002 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1527) covalent geometry : angle 0.87890 ( 2043) hydrogen bonds : bond 0.01514 ( 28) hydrogen bonds : angle 3.51611 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 308 ILE cc_start: 0.7427 (tt) cc_final: 0.7197 (mt) REVERT: E 310 TYR cc_start: 0.8261 (t80) cc_final: 0.7670 (t80) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.0914 time to fit residues: 2.1981 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.137861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.125884 restraints weight = 7172.917| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.27 r_work: 0.4337 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4257 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.116 Angle : 0.895 11.189 2043 Z= 0.468 Chirality : 0.218 1.482 237 Planarity : 0.004 0.034 258 Dihedral : 5.540 15.861 204 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 17.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 310 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1527) covalent geometry : angle 0.89458 ( 2043) hydrogen bonds : bond 0.01541 ( 28) hydrogen bonds : angle 3.45467 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: C 284 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7258 (mp) REVERT: E 310 TYR cc_start: 0.8259 (t80) cc_final: 0.7661 (t80) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.0991 time to fit residues: 2.3879 Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.133411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.121310 restraints weight = 7449.662| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.27 r_work: 0.4277 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1527 Z= 0.139 Angle : 0.916 11.364 2043 Z= 0.480 Chirality : 0.219 1.512 237 Planarity : 0.004 0.035 258 Dihedral : 6.006 16.797 204 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.11 % Allowed : 17.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 310 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 1527) covalent geometry : angle 0.91601 ( 2043) hydrogen bonds : bond 0.01439 ( 28) hydrogen bonds : angle 3.34073 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.37 seconds wall clock time: 24 minutes 14.20 seconds (1454.20 seconds total)