Starting phenix.real_space_refine on Fri Aug 22 12:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo7_19846/08_2025/9eo7_19846.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 372 2.51 5 N 109 2.21 5 O 112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 595 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} bond proxies already assigned to first conformer: 588 Time building chain proxies: 0.47, per 1000 atoms: 0.79 Number of scatterers: 595 At special positions: 0 Unit cell: (70.864, 84.048, 23.072, 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 2 16.00 O 112 8.00 N 109 7.00 C 372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.03 Conformation dependent library (CDL) restraints added in 49.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 154 1.34 - 1.46: 145 1.46 - 1.58: 303 1.58 - 1.70: 0 1.70 - 1.82: 3 Bond restraints: 605 Sorted by residual: bond pdb=" C GLN A 336 " pdb=" N BVAL A 337 " ideal model delta sigma weight residual 1.331 1.406 -0.075 1.27e-02 6.20e+03 3.52e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.75e+01 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CA SER A 316 " pdb=" CB SER A 316 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.66e-02 3.63e+03 7.04e+00 bond pdb=" CE1 HIS A 330 " pdb=" NE2 HIS A 330 " ideal model delta sigma weight residual 1.321 1.295 0.026 1.00e-02 1.00e+04 6.66e+00 ... (remaining 600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 624 1.67 - 3.34: 145 3.34 - 5.01: 33 5.01 - 6.68: 6 6.68 - 8.35: 2 Bond angle restraints: 810 Sorted by residual: angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.73 120.08 -8.35 1.42e+00 4.96e-01 3.46e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 131.20 125.05 6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" ND1 HIS A 330 " ideal model delta sigma weight residual 122.70 129.39 -6.69 1.50e+00 4.44e-01 1.99e+01 angle pdb=" CA THR A 361 " pdb=" CB THR A 361 " pdb=" OG1 THR A 361 " ideal model delta sigma weight residual 109.60 103.04 6.56 1.50e+00 4.44e-01 1.91e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 115.84 -5.15 1.33e+00 5.65e-01 1.50e+01 ... (remaining 805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.86: 263 7.86 - 15.71: 70 15.71 - 23.57: 20 23.57 - 31.43: 12 31.43 - 39.28: 5 Dihedral angle restraints: 370 sinusoidal: 155 harmonic: 215 Sorted by residual: dihedral pdb=" C ARG A 349 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta harmonic sigma weight residual -122.60 -135.14 12.54 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" CA SER A 352 " pdb=" C SER A 352 " pdb=" N LYS A 353 " pdb=" CA LYS A 353 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ARG A 379 " pdb=" C ARG A 379 " pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 367 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.077: 46 0.077 - 0.151: 36 0.151 - 0.226: 7 0.226 - 0.300: 0 0.300 - 0.375: 1 Chirality restraints: 90 Sorted by residual: chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA AMET A 337 " pdb=" N AMET A 337 " pdb=" C AMET A 337 " pdb=" CB AMET A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 87 not shown) Planarity restraints: 104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 336 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLN A 336 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN A 336 " -0.018 2.00e-02 2.50e+03 pdb=" N BVAL A 337 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ARG A 349 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG A 349 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 350 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.028 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 101 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 308 3.05 - 3.51: 481 3.51 - 3.97: 687 3.97 - 4.44: 515 4.44 - 4.90: 1012 Nonbonded interactions: 3003 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.583 3.040 nonbonded pdb=" O GLY A 334 " pdb=" CA GLY A 335 " model vdw 2.662 2.752 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.667 3.120 nonbonded pdb=" N ASN A 368 " pdb=" O ASN A 368 " model vdw 2.668 2.496 nonbonded pdb=" O LEU A 325 " pdb=" CA GLY A 326 " model vdw 2.674 2.752 ... (remaining 2998 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: 4.380 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: 0.010 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.470 Find NCS groups from input model: 0.000 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.009 0.075 605 Z= 0.670 Angle : 1.590 8.348 810 Z= 1.025 Chirality : 0.095 0.375 90 Planarity : 0.009 0.032 104 Dihedral : 12.220 39.283 234 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.47 % Allowed : 8.82 % Favored : 89.71 % Cbeta Deviations : 1.47 % 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 aren not related in a simple way. whole: -4.16 (0.58), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.44), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.038 0.011 TYR A 310 PHE 0.032 0.008 PHE A 346 HIS 0.009 0.003 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00923 ( 605) covalent geometry : angle 1.59007 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8399 (ttpt) REVERT: A 343 LYS cc_start: 0.8476 (mttp) cc_final: 0.8072 (mtpp) REVERT: A 349 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7588 (ptm160) REVERT: A 375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7950 (ttmp) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.6147 time to fit residues: 10.5347 Evaluate side-chains 12 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 330 HIS A 368 ASN A 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.206512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.184397 restraints weight = 4331.164| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 5.75 r_work: 0.4242 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4267 r_free = 0.4267 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4278 r_free = 0.4278 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 605 Z= 0.104 Angle : 0.540 5.057 810 Z= 0.273 Chirality : 0.049 0.129 90 Planarity : 0.004 0.025 104 Dihedral : 5.179 13.747 81 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % 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 aren not related in a simple way. whole: -3.01 (0.73), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.002 0.001 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 605) covalent geometry : angle 0.54005 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8418 (mttp) cc_final: 0.8032 (mtpp) REVERT: A 348 ASP cc_start: 0.8528 (t0) cc_final: 0.7767 (m-30) REVERT: A 358 ASP cc_start: 0.8467 (p0) cc_final: 0.8086 (m-30) REVERT: A 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7814 (ttmt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.6919 time to fit residues: 8.3755 Evaluate side-chains 8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 overall best weight: 1.6717 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.176807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.155659 restraints weight = 4307.541| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 5.16 r_work: 0.4171 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4162 r_free = 0.4162 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 605 Z= 0.131 Angle : 0.552 5.139 810 Z= 0.280 Chirality : 0.049 0.134 90 Planarity : 0.004 0.033 104 Dihedral : 4.797 12.479 81 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.47 % Allowed : 14.71 % Favored : 83.82 % 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 aren not related in a simple way. whole: -2.43 (0.78), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.60), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.006 0.002 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 605) covalent geometry : angle 0.55209 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.026 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 7 average time/residue: 0.4466 time to fit residues: 3.1850 Evaluate side-chains 7 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 overall best weight: 1.3517 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.176514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.158625 restraints weight = 3906.590| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 4.33 r_work: 0.4238 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4210 r_free = 0.4210 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4210 r_free = 0.4210 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 605 Z= 0.114 Angle : 0.503 4.747 810 Z= 0.256 Chirality : 0.048 0.128 90 Planarity : 0.004 0.035 104 Dihedral : 4.515 11.664 81 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % 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 aren not related in a simple way. whole: -2.17 (0.82), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.007 0.002 TYR A 310 PHE 0.002 0.001 PHE A 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 605) covalent geometry : angle 0.50321 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.027 Fit side-chains REVERT: A 342 GLU cc_start: 0.5318 (OUTLIER) cc_final: 0.3235 (mp0) REVERT: A 348 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7486 (m-30) outliers start: 2 outliers final: 0 residues processed: 9 average time/residue: 0.3301 time to fit residues: 3.0365 Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 overall best weight: 2.0320 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.170748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.149831 restraints weight = 4536.189| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 5.01 r_work: 0.4147 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 605 Z= 0.149 Angle : 0.527 4.765 810 Z= 0.271 Chirality : 0.049 0.136 90 Planarity : 0.004 0.039 104 Dihedral : 4.731 11.981 81 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % 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 aren not related in a simple way. whole: -2.00 (0.83), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.010 0.003 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 605) covalent geometry : angle 0.52717 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.027 Fit side-chains REVERT: A 342 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5259 (mp0) REVERT: A 348 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: A 379 ARG cc_start: 0.8543 (mpt-90) cc_final: 0.6456 (pmt170) outliers start: 2 outliers final: 0 residues processed: 8 average time/residue: 0.5948 time to fit residues: 4.8199 Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.8983 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.171310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.150078 restraints weight = 5150.218| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 5.24 r_work: 0.4144 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 605 Z= 0.140 Angle : 0.509 4.556 810 Z= 0.261 Chirality : 0.048 0.133 90 Planarity : 0.004 0.037 104 Dihedral : 4.629 11.321 81 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.41 % Allowed : 16.18 % Favored : 79.41 % 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 aren not related in a simple way. whole: -1.93 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.009 0.003 TYR A 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 605) covalent geometry : angle 0.50909 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.024 Fit side-chains REVERT: A 348 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: A 379 ARG cc_start: 0.8574 (mpt-90) cc_final: 0.6498 (pmt170) outliers start: 3 outliers final: 1 residues processed: 10 average time/residue: 0.5641 time to fit residues: 5.7068 Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.3323 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.169488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.147681 restraints weight = 5631.160| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 5.63 r_work: 0.4162 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 605 Z= 0.167 Angle : 0.550 4.655 810 Z= 0.286 Chirality : 0.048 0.138 90 Planarity : 0.005 0.046 104 Dihedral : 4.746 11.557 81 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % 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 aren not related in a simple way. whole: -1.97 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.012 0.003 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 605) covalent geometry : angle 0.54961 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.028 Fit side-chains REVERT: A 348 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: A 379 ARG cc_start: 0.8598 (mpt-90) cc_final: 0.6572 (pmt170) outliers start: 2 outliers final: 1 residues processed: 9 average time/residue: 0.4238 time to fit residues: 3.8814 Evaluate side-chains 10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3977 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.203837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.182293 restraints weight = 4372.741| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 5.09 r_work: 0.4250 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4254 r_free = 0.4254 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4254 r_free = 0.4254 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 605 Z= 0.084 Angle : 0.457 4.020 810 Z= 0.238 Chirality : 0.048 0.115 90 Planarity : 0.005 0.047 104 Dihedral : 4.096 11.095 81 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.94 % Allowed : 19.12 % Favored : 77.94 % 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 aren not related in a simple way. whole: -1.93 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.004 0.001 TYR A 310 PHE 0.002 0.000 PHE A 346 HIS 0.001 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 605) covalent geometry : angle 0.45652 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.031 Fit side-chains REVERT: A 348 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 379 ARG cc_start: 0.8524 (mpt-90) cc_final: 0.6540 (ppt170) outliers start: 2 outliers final: 1 residues processed: 10 average time/residue: 0.4167 time to fit residues: 4.2365 Evaluate side-chains 11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.203097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.181385 restraints weight = 5210.435| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 5.32 r_work: 0.4258 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4242 r_free = 0.4242 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4242 r_free = 0.4242 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 605 Z= 0.086 Angle : 0.467 4.071 810 Z= 0.239 Chirality : 0.048 0.120 90 Planarity : 0.005 0.051 104 Dihedral : 4.012 11.435 81 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.47 % Allowed : 20.59 % Favored : 77.94 % 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 aren not related in a simple way. whole: -1.84 (0.85), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.005 0.001 TYR A 310 PHE 0.002 0.001 PHE A 346 HIS 0.001 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 605) covalent geometry : angle 0.46659 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.016 Fit side-chains REVERT: A 348 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: A 379 ARG cc_start: 0.8553 (mpt-90) cc_final: 0.6611 (ppt170) outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.4680 time to fit residues: 4.7363 Evaluate side-chains 10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3317 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.197021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.177051 restraints weight = 5581.555| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 5.91 r_work: 0.4181 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 605 Z= 0.115 Angle : 0.494 4.294 810 Z= 0.255 Chirality : 0.048 0.128 90 Planarity : 0.006 0.053 104 Dihedral : 4.239 10.725 81 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 20.59 % Favored : 77.94 % 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 aren not related in a simple way. whole: -1.72 (0.88), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.008 0.002 TYR A 310 PHE 0.002 0.001 PHE A 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 605) covalent geometry : angle 0.49434 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.024 Fit side-chains REVERT: A 348 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: A 379 ARG cc_start: 0.8584 (mpt-90) cc_final: 0.6587 (ppt170) outliers start: 1 outliers final: 1 residues processed: 8 average time/residue: 0.3644 time to fit residues: 2.9718 Evaluate side-chains 9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5983 ------------------------------------------------------------------------------- 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 = 0.4578 r_free = 0.4578 target = 0.199259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.178859 restraints weight = 2302.854| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 3.98 r_work: 0.4269 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 605 Z= 0.091 Angle : 0.471 4.248 810 Z= 0.243 Chirality : 0.048 0.123 90 Planarity : 0.006 0.053 104 Dihedral : 4.166 10.895 81 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.94 % Allowed : 19.12 % Favored : 77.94 % 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 aren not related in a simple way. whole: -1.78 (0.86), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.005 0.001 TYR A 310 PHE 0.002 0.001 PHE A 346 HIS 0.001 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 605) covalent geometry : angle 0.47117 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 560.93 seconds wall clock time: 10 minutes 28.55 seconds (628.55 seconds total)