Starting phenix.real_space_refine on Wed Sep 17 03:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207.map" model { file = "/net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vhl_21207/09_2025/6vhl_21207_neut.cif" } resolution = 3.3 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 742 2.51 5 N 220 2.21 5 O 226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1190 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Time building chain proxies: 0.60, per 1000 atoms: 0.50 Number of scatterers: 1190 At special positions: 0 Unit cell: (146.64, 78, 28.08, 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 226 8.00 N 220 7.00 C 742 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: 0.20 Conformation dependent library (CDL) restraints added in 90.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 268 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: 0.24 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: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 393 1.34 - 1.46: 184 1.46 - 1.57: 627 1.57 - 1.69: 0 1.69 - 1.80: 2 Bond restraints: 1206 Sorted by residual: bond pdb=" N ARG F 379 " pdb=" CA ARG F 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N ARG E 379 " pdb=" CA ARG E 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 bond pdb=" N LYS F 370 " pdb=" CA LYS F 370 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.20e-02 6.94e+03 6.51e+00 bond pdb=" CE LYS E 370 " pdb=" NZ LYS E 370 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.43e+00 bond pdb=" N LYS F 369 " pdb=" CA LYS F 369 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.27e-02 6.20e+03 4.03e+00 ... (remaining 1201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 1470 1.59 - 3.19: 102 3.19 - 4.78: 29 4.78 - 6.37: 2 6.37 - 7.96: 5 Bond angle restraints: 1608 Sorted by residual: angle pdb=" N LYS E 369 " pdb=" CA LYS E 369 " pdb=" CB LYS E 369 " ideal model delta sigma weight residual 110.44 117.19 -6.75 1.43e+00 4.89e-01 2.23e+01 angle pdb=" N LYS F 369 " pdb=" CA LYS F 369 " pdb=" C LYS F 369 " ideal model delta sigma weight residual 110.50 105.97 4.53 1.41e+00 5.03e-01 1.03e+01 angle pdb=" CA GLY E 367 " pdb=" C GLY E 367 " pdb=" N ASN E 368 " ideal model delta sigma weight residual 116.69 110.25 6.44 2.04e+00 2.40e-01 9.96e+00 angle pdb=" C THR E 377 " pdb=" N PHE E 378 " pdb=" CA PHE E 378 " ideal model delta sigma weight residual 122.67 126.92 -4.25 1.47e+00 4.63e-01 8.37e+00 angle pdb=" C THR F 377 " pdb=" N PHE F 378 " pdb=" CA PHE F 378 " ideal model delta sigma weight residual 122.67 126.91 -4.24 1.47e+00 4.63e-01 8.33e+00 ... (remaining 1603 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 12.67: 592 12.67 - 25.32: 86 25.32 - 37.98: 27 37.98 - 50.64: 17 50.64 - 63.29: 6 Dihedral angle restraints: 728 sinusoidal: 304 harmonic: 424 Sorted by residual: dihedral pdb=" C GLU F 380 " pdb=" N GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual -122.60 -132.58 9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C GLU E 380 " pdb=" N GLU E 380 " pdb=" CA GLU E 380 " pdb=" CB GLU E 380 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 725 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.084: 147 0.084 - 0.167: 26 0.167 - 0.249: 3 0.249 - 0.332: 0 0.332 - 0.415: 2 Chirality restraints: 178 Sorted by residual: chirality pdb=" CA GLU F 380 " pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CB GLU F 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA GLU E 380 " pdb=" N GLU E 380 " pdb=" C GLU E 380 " pdb=" CB GLU E 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PHE E 378 " pdb=" N PHE E 378 " pdb=" C PHE E 378 " pdb=" CB PHE E 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 175 not shown) Planarity restraints: 206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 367 " -0.024 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C GLY E 367 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY E 367 " -0.035 2.00e-02 2.50e+03 pdb=" N ASN E 368 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 367 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C GLY F 367 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY F 367 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 368 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO E 332 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.027 5.00e-02 4.00e+02 ... (remaining 203 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 7 2.41 - 3.03: 635 3.03 - 3.66: 1387 3.66 - 4.28: 1677 4.28 - 4.90: 2417 Nonbonded interactions: 6123 Sorted by model distance: nonbonded pdb=" NZ LYS E 317 " pdb=" O GLY E 402 " model vdw 1.791 3.120 nonbonded pdb=" NZ LYS F 317 " pdb=" O GLY F 402 " model vdw 1.807 3.120 nonbonded pdb=" CE LYS F 317 " pdb=" O GLY F 402 " model vdw 1.970 3.440 nonbonded pdb=" CE LYS E 317 " pdb=" O GLY E 402 " model vdw 1.974 3.440 nonbonded pdb=" OG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 2.392 3.040 ... (remaining 6118 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 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.860 Find NCS groups from input model: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.007 0.063 1206 Z= 0.362 Angle : 1.031 7.962 1608 Z= 0.579 Chirality : 0.072 0.415 178 Planarity : 0.008 0.051 206 Dihedral : 15.846 63.293 460 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % 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: -6.30 (0.40), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.30), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.007 0.003 TYR E 310 PHE 0.003 0.001 PHE F 346 HIS 0.002 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 1206) covalent geometry : angle 1.03124 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.053 Fit side-chains REVERT: E 311 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8216 (mtpt) REVERT: E 349 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5879 (ptt-90) REVERT: F 375 LYS cc_start: 0.8511 (mttt) cc_final: 0.8303 (pptt) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1137 time to fit residues: 5.5436 Evaluate side-chains 34 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.0170 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.152691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.141984 restraints weight = 2838.160| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 4.17 r_work: 0.4349 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1206 Z= 0.125 Angle : 0.646 6.020 1608 Z= 0.323 Chirality : 0.049 0.129 178 Planarity : 0.005 0.039 206 Dihedral : 8.849 54.305 172 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.48 % Allowed : 12.69 % Favored : 82.84 % 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: -5.14 (0.48), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.37), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 349 TYR 0.003 0.001 TYR F 310 PHE 0.003 0.001 PHE E 346 HIS 0.002 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1206) covalent geometry : angle 0.64551 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.051 Fit side-chains REVERT: E 311 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8462 (mtpt) REVERT: E 349 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6353 (mmp-170) REVERT: E 376 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7118 (tp) REVERT: F 340 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7731 (mmtm) REVERT: F 375 LYS cc_start: 0.8547 (mttt) cc_final: 0.8339 (pptt) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.0973 time to fit residues: 4.5655 Evaluate side-chains 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.150891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.140307 restraints weight = 2899.162| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 4.36 r_work: 0.4292 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1206 Z= 0.120 Angle : 0.591 5.066 1608 Z= 0.296 Chirality : 0.046 0.117 178 Planarity : 0.004 0.040 206 Dihedral : 7.220 52.660 166 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 6.72 % Allowed : 14.93 % Favored : 78.36 % 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: -4.41 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.002 0.001 TYR F 310 PHE 0.002 0.001 PHE E 378 HIS 0.005 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 1206) covalent geometry : angle 0.59067 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.051 Fit side-chains REVERT: E 311 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8265 (mmtt) REVERT: E 349 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.6550 (mmp-170) REVERT: F 340 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7970 (mmtm) REVERT: F 349 ARG cc_start: 0.5471 (ptt-90) cc_final: 0.4767 (mmp-170) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.0827 time to fit residues: 4.2711 Evaluate side-chains 43 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.152167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.141867 restraints weight = 3039.408| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 4.35 r_work: 0.4329 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1206 Z= 0.109 Angle : 0.583 5.910 1608 Z= 0.291 Chirality : 0.045 0.115 178 Planarity : 0.004 0.035 206 Dihedral : 6.292 46.200 164 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.48 % Allowed : 20.15 % Favored : 75.37 % 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: -4.12 (0.56), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.001 0.000 TYR E 310 PHE 0.003 0.001 PHE F 346 HIS 0.008 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 1206) covalent geometry : angle 0.58276 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.051 Fit side-chains REVERT: E 311 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8294 (mmtt) REVERT: E 349 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.6488 (mmp-170) REVERT: F 349 ARG cc_start: 0.5491 (ptt-90) cc_final: 0.4816 (mmp-170) REVERT: F 351 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8503 (pt0) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.0959 time to fit residues: 4.5010 Evaluate side-chains 38 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.155473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.145046 restraints weight = 2959.618| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 4.37 r_work: 0.4346 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1206 Z= 0.099 Angle : 0.575 5.875 1608 Z= 0.276 Chirality : 0.044 0.116 178 Planarity : 0.004 0.035 206 Dihedral : 4.632 17.361 160 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.99 % Allowed : 23.13 % Favored : 73.88 % 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: -3.83 (0.59), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.002 0.000 TYR E 310 PHE 0.002 0.001 PHE F 346 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1206) covalent geometry : angle 0.57493 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.051 Fit side-chains REVERT: E 311 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8321 (mmtt) REVERT: E 349 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.6464 (mmp-170) REVERT: F 349 ARG cc_start: 0.5388 (ptt-90) cc_final: 0.4754 (mmp-170) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.0907 time to fit residues: 3.9055 Evaluate side-chains 37 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 = 0.4573 r_free = 0.4573 target = 0.156014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.146088 restraints weight = 2936.773| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 4.21 r_work: 0.4361 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1206 Z= 0.090 Angle : 0.532 5.109 1608 Z= 0.257 Chirality : 0.044 0.115 178 Planarity : 0.003 0.029 206 Dihedral : 4.260 17.123 160 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.99 % Allowed : 26.87 % Favored : 70.15 % 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: -3.57 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.002 0.000 TYR E 310 PHE 0.002 0.000 PHE F 346 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 1206) covalent geometry : angle 0.53218 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.050 Fit side-chains REVERT: E 311 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8248 (mmtt) REVERT: E 349 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.6508 (mmp-170) REVERT: E 378 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5923 (t80) REVERT: F 338 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7996 (mp0) REVERT: F 349 ARG cc_start: 0.5548 (ptt-90) cc_final: 0.5107 (mmp-170) REVERT: F 351 GLN cc_start: 0.8743 (pt0) cc_final: 0.8432 (pt0) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1043 time to fit residues: 4.5482 Evaluate side-chains 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 PHE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.153270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.143243 restraints weight = 2980.728| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 4.24 r_work: 0.4329 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1206 Z= 0.119 Angle : 0.551 4.882 1608 Z= 0.269 Chirality : 0.044 0.115 178 Planarity : 0.003 0.028 206 Dihedral : 4.457 16.650 160 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.24 % Allowed : 28.36 % Favored : 69.40 % 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: -3.38 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG E 379 TYR 0.001 0.000 TYR E 310 PHE 0.001 0.000 PHE E 378 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 1206) covalent geometry : angle 0.55098 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.052 Fit side-chains REVERT: E 311 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8260 (mmtt) REVERT: E 349 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.6509 (mmp-170) REVERT: E 378 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6541 (t80) REVERT: F 340 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8181 (mmtm) REVERT: F 343 LYS cc_start: 0.5108 (tppt) cc_final: 0.4840 (tppt) REVERT: F 349 ARG cc_start: 0.5571 (ptt-90) cc_final: 0.5111 (mmp-170) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1002 time to fit residues: 3.8517 Evaluate side-chains 34 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 PHE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 3 optimal weight: 0.0050 chunk 12 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.154347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.144333 restraints weight = 2943.252| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 4.21 r_work: 0.4346 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1206 Z= 0.112 Angle : 0.631 6.364 1608 Z= 0.296 Chirality : 0.044 0.112 178 Planarity : 0.003 0.021 206 Dihedral : 4.361 16.833 160 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.48 % Allowed : 26.12 % Favored : 69.40 % 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: -3.34 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.001 0.000 TYR E 310 PHE 0.002 0.000 PHE E 378 HIS 0.004 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 1206) covalent geometry : angle 0.63135 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.060 Fit side-chains REVERT: E 311 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8304 (mmtt) REVERT: E 343 LYS cc_start: 0.5518 (tppt) cc_final: 0.5043 (tppt) REVERT: E 349 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.6523 (mmp-170) REVERT: F 349 ARG cc_start: 0.5701 (ptt-90) cc_final: 0.5206 (mmp-170) REVERT: F 358 ASP cc_start: 0.8590 (p0) cc_final: 0.7716 (m-30) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.0944 time to fit residues: 3.6542 Evaluate side-chains 35 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 0.0030 chunk 9 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.147998 restraints weight = 2904.683| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 4.20 r_work: 0.4390 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1206 Z= 0.109 Angle : 0.664 6.458 1608 Z= 0.307 Chirality : 0.045 0.113 178 Planarity : 0.003 0.028 206 Dihedral : 3.953 17.572 160 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.24 % Allowed : 28.36 % Favored : 69.40 % 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: -3.26 (0.62), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.001 0.000 TYR E 310 PHE 0.001 0.000 PHE F 346 HIS 0.004 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1206) covalent geometry : angle 0.66422 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.061 Fit side-chains REVERT: E 311 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8291 (mmtt) REVERT: E 343 LYS cc_start: 0.5611 (tppt) cc_final: 0.5177 (tppt) REVERT: E 349 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.6543 (mmp-170) REVERT: F 343 LYS cc_start: 0.4922 (tppt) cc_final: 0.4672 (tppt) REVERT: F 349 ARG cc_start: 0.5834 (ptt-90) cc_final: 0.5423 (mtp180) REVERT: F 358 ASP cc_start: 0.8560 (p0) cc_final: 0.7632 (m-30) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0969 time to fit residues: 3.8548 Evaluate side-chains 36 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.0770 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.144567 restraints weight = 2937.007| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 4.30 r_work: 0.4362 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1206 Z= 0.117 Angle : 0.664 5.828 1608 Z= 0.314 Chirality : 0.044 0.111 178 Planarity : 0.003 0.019 206 Dihedral : 4.060 16.275 160 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.99 % Allowed : 26.87 % Favored : 70.15 % 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: -3.17 (0.62), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.002 0.000 TYR E 310 PHE 0.001 0.000 PHE F 346 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1206) covalent geometry : angle 0.66403 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.054 Fit side-chains REVERT: E 311 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8333 (mmtt) REVERT: E 343 LYS cc_start: 0.5426 (tppt) cc_final: 0.4983 (tppt) REVERT: E 349 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.6529 (mmp-170) REVERT: F 343 LYS cc_start: 0.4961 (tppt) cc_final: 0.4685 (tppt) REVERT: F 349 ARG cc_start: 0.5740 (ptt-90) cc_final: 0.5245 (mmp-170) REVERT: F 358 ASP cc_start: 0.8545 (p0) cc_final: 0.7610 (m-30) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.0974 time to fit residues: 3.6543 Evaluate side-chains 36 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.154515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.144037 restraints weight = 2922.042| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 4.25 r_work: 0.4358 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1206 Z= 0.111 Angle : 0.626 5.833 1608 Z= 0.294 Chirality : 0.044 0.111 178 Planarity : 0.003 0.016 206 Dihedral : 4.087 16.047 160 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.99 % Allowed : 26.87 % Favored : 70.15 % 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: -3.11 (0.63), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.001 0.000 TYR E 310 PHE 0.001 0.000 PHE F 346 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1206) covalent geometry : angle 0.62562 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 629.35 seconds wall clock time: 11 minutes 25.32 seconds (685.32 seconds total)