Starting phenix.real_space_refine on Wed Mar 5 14:16:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vhl_21207/03_2025/6vhl_21207_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vhl_21207/03_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_21207/03_2025/6vhl_21207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vhl_21207/03_2025/6vhl_21207.map" model { file = "/net/cci-nas-00/data/ceres_data/6vhl_21207/03_2025/6vhl_21207_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vhl_21207/03_2025/6vhl_21207_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 1.28, per 1000 atoms: 1.08 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: 0.60 Conformation dependent library (CDL) restraints added in 186.0 milliseconds 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: 0.70 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: 0.66 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: 0.01 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: 0.730 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS F 330 PHE 0.003 0.001 PHE F 346 TYR 0.007 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** 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 : 0.147 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: 0.5829 (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: 0.2546 time to fit residues: 12.4570 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 : 0.171 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.153967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.143749 restraints weight = 2939.707| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 4.05 r_work: 0.4342 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4143 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= 0.134 Angle : 0.656 6.069 1608 Z= 0.329 Chirality : 0.049 0.130 178 Planarity : 0.005 0.039 206 Dihedral : 8.979 54.437 172 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.22 % Allowed : 11.19 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.48), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.37), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.003 0.001 PHE E 378 TYR 0.003 0.001 TYR F 310 ARG 0.003 0.000 ARG F 349 *********************** 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 47 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.134 Fit side-chains REVERT: E 311 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8470 (mtpt) REVERT: E 349 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.6500 (mmp-170) REVERT: F 340 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7779 (mmtm) REVERT: F 370 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7820 (tptp) REVERT: F 375 LYS cc_start: 0.8551 (mttt) cc_final: 0.8350 (pptt) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.2167 time to fit residues: 9.9229 Evaluate side-chains 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.149692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.139344 restraints weight = 2868.513| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 4.25 r_work: 0.4298 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5297 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= 0.130 Angle : 0.595 4.894 1608 Z= 0.300 Chirality : 0.046 0.116 178 Planarity : 0.005 0.040 206 Dihedral : 7.273 51.727 170 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.97 % Allowed : 14.18 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.003 0.001 PHE F 346 TYR 0.003 0.001 TYR F 310 ARG 0.002 0.001 ARG F 379 *********************** 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 56 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.149 Fit side-chains REVERT: E 311 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8262 (mmtt) REVERT: E 349 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.6455 (mmp-170) REVERT: F 340 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8063 (mmtm) REVERT: F 349 ARG cc_start: 0.5498 (ptt-90) cc_final: 0.4775 (mmp-170) REVERT: F 375 LYS cc_start: 0.8551 (mttt) cc_final: 0.8315 (pptt) outliers start: 8 outliers final: 2 residues processed: 50 average time/residue: 0.1870 time to fit residues: 10.0419 Evaluate side-chains 46 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.150037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.139526 restraints weight = 2958.013| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 4.31 r_work: 0.4293 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1206 Z= 0.107 Angle : 0.593 6.639 1608 Z= 0.285 Chirality : 0.045 0.113 178 Planarity : 0.004 0.034 206 Dihedral : 6.019 44.036 164 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.99 % Allowed : 20.90 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.58), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.004 0.001 PHE E 378 TYR 0.002 0.001 TYR F 310 ARG 0.001 0.001 ARG E 379 *********************** 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 49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.139 Fit side-chains REVERT: E 311 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8362 (mmtt) REVERT: E 349 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.6515 (mmp-170) REVERT: F 311 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8431 (mmtt) REVERT: F 340 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8104 (mmtm) REVERT: F 349 ARG cc_start: 0.5464 (ptt-90) cc_final: 0.4709 (mmp-170) REVERT: F 351 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: F 372 GLU cc_start: 0.7619 (mp0) cc_final: 0.7407 (mp0) REVERT: F 375 LYS cc_start: 0.8565 (mttt) cc_final: 0.8297 (pptt) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.2012 time to fit residues: 10.3511 Evaluate side-chains 43 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 overall best weight: 0.1836 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.153841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.143672 restraints weight = 2913.052| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 4.32 r_work: 0.4345 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1206 Z= 0.090 Angle : 0.576 5.922 1608 Z= 0.270 Chirality : 0.045 0.114 178 Planarity : 0.004 0.034 206 Dihedral : 4.389 17.482 160 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.24 % Allowed : 25.37 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 329 PHE 0.003 0.001 PHE E 346 TYR 0.002 0.000 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** 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 45 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.138 Fit side-chains REVERT: E 311 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8341 (mmtt) REVERT: E 349 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.6489 (mmp-170) REVERT: E 378 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6156 (t80) REVERT: F 311 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8406 (mmtt) REVERT: F 340 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8238 (mmtm) REVERT: F 349 ARG cc_start: 0.5284 (ptt-90) cc_final: 0.4752 (mmp-170) REVERT: F 351 GLN cc_start: 0.8745 (pt0) cc_final: 0.8426 (pt0) REVERT: F 375 LYS cc_start: 0.8559 (mttt) cc_final: 0.8193 (pptt) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.1918 time to fit residues: 8.8810 Evaluate side-chains 44 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.148114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.137630 restraints weight = 2906.047| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 4.30 r_work: 0.4275 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1206 Z= 0.154 Angle : 0.618 5.643 1608 Z= 0.299 Chirality : 0.044 0.116 178 Planarity : 0.003 0.027 206 Dihedral : 4.850 16.521 160 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.48 % Allowed : 23.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.002 0.001 PHE E 378 TYR 0.002 0.001 TYR E 310 ARG 0.002 0.001 ARG F 379 *********************** 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 45 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.149 Fit side-chains REVERT: E 311 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8358 (mmtt) REVERT: E 349 ARG cc_start: 0.7684 (mtp-110) cc_final: 0.6504 (mmp-170) REVERT: F 340 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8174 (mmtm) REVERT: F 349 ARG cc_start: 0.5488 (ptt-90) cc_final: 0.4814 (mmp-170) REVERT: F 353 LYS cc_start: 0.8808 (mttt) cc_final: 0.8561 (mtpt) REVERT: F 375 LYS cc_start: 0.8600 (mttt) cc_final: 0.8280 (pptt) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.2151 time to fit residues: 9.4475 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.150509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.139975 restraints weight = 2888.573| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 4.36 r_work: 0.4291 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.7160 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= 0.112 Angle : 0.634 7.615 1608 Z= 0.287 Chirality : 0.044 0.112 178 Planarity : 0.003 0.024 206 Dihedral : 4.558 17.772 160 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.73 % Allowed : 25.37 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.001 0.000 PHE F 378 TYR 0.002 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** 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 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.150 Fit side-chains REVERT: E 311 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8345 (mmtt) REVERT: E 349 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.6367 (mmp-170) REVERT: F 311 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8422 (mmtt) REVERT: F 343 LYS cc_start: 0.4927 (tppt) cc_final: 0.4647 (tppt) REVERT: F 349 ARG cc_start: 0.5627 (ptt-90) cc_final: 0.4979 (mmp-170) REVERT: F 353 LYS cc_start: 0.8828 (mttt) cc_final: 0.8580 (mtpt) REVERT: F 375 LYS cc_start: 0.8599 (mttt) cc_final: 0.8184 (pptt) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.2191 time to fit residues: 8.6948 Evaluate side-chains 38 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.0020 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.152008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.141496 restraints weight = 2932.052| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 4.35 r_work: 0.4303 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1206 Z= 0.105 Angle : 0.618 7.233 1608 Z= 0.282 Chirality : 0.044 0.112 178 Planarity : 0.003 0.026 206 Dihedral : 4.312 17.814 160 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.001 0.000 PHE F 378 TYR 0.002 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** 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 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.153 Fit side-chains REVERT: E 311 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8315 (mmtt) REVERT: E 349 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.6412 (mmp-170) REVERT: F 311 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8403 (mmtt) REVERT: F 349 ARG cc_start: 0.5512 (ptt-90) cc_final: 0.4832 (mmp-170) REVERT: F 353 LYS cc_start: 0.8808 (mttt) cc_final: 0.8566 (mtpt) REVERT: F 358 ASP cc_start: 0.8599 (p0) cc_final: 0.7668 (m-30) REVERT: F 375 LYS cc_start: 0.8580 (mttt) cc_final: 0.8195 (pptt) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.2140 time to fit residues: 8.7239 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER 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 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 3 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.149941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.139022 restraints weight = 2892.918| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 4.42 r_work: 0.4297 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1206 Z= 0.109 Angle : 0.626 7.008 1608 Z= 0.286 Chirality : 0.044 0.112 178 Planarity : 0.003 0.021 206 Dihedral : 4.153 17.548 160 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.73 % Allowed : 26.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.62), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.001 0.000 PHE E 378 TYR 0.002 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** 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 40 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.130 Fit side-chains REVERT: E 311 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8353 (mmtt) REVERT: E 349 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6369 (mmp-170) REVERT: F 311 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8413 (mmtt) REVERT: F 340 LYS cc_start: 0.8637 (tptp) cc_final: 0.7680 (pttm) REVERT: F 343 LYS cc_start: 0.4919 (tppt) cc_final: 0.4556 (tppt) REVERT: F 349 ARG cc_start: 0.5711 (ptt-90) cc_final: 0.4986 (mmp-170) REVERT: F 353 LYS cc_start: 0.8839 (mttt) cc_final: 0.8614 (mtpt) REVERT: F 358 ASP cc_start: 0.8536 (p0) cc_final: 0.7516 (m-30) REVERT: F 375 LYS cc_start: 0.8605 (mttt) cc_final: 0.8202 (pptt) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1996 time to fit residues: 8.5434 Evaluate side-chains 40 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.148890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.138002 restraints weight = 2870.811| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 4.32 r_work: 0.4286 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1206 Z= 0.142 Angle : 0.647 6.748 1608 Z= 0.302 Chirality : 0.044 0.110 178 Planarity : 0.003 0.022 206 Dihedral : 4.309 17.166 160 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.99 % Allowed : 26.12 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.63), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.002 0.001 PHE E 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.001 ARG E 379 ********************** 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 : 0.148 Fit side-chains REVERT: E 311 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8390 (mmtt) REVERT: E 349 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.6400 (mmp-170) REVERT: F 311 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8444 (mmtt) REVERT: F 343 LYS cc_start: 0.4993 (tppt) cc_final: 0.4633 (tppt) REVERT: F 349 ARG cc_start: 0.5755 (ptt-90) cc_final: 0.5022 (mmp-170) REVERT: F 353 LYS cc_start: 0.8904 (mttt) cc_final: 0.8672 (mtpt) REVERT: F 358 ASP cc_start: 0.8553 (p0) cc_final: 0.7529 (m-30) REVERT: F 375 LYS cc_start: 0.8624 (mttt) cc_final: 0.8223 (pptt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.2110 time to fit residues: 8.3884 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 : 0.140 ------------------------------------------------------------------------------- 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 352 SER 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 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.150739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.140189 restraints weight = 2962.551| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 4.24 r_work: 0.4292 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1206 Z= 0.115 Angle : 0.627 6.823 1608 Z= 0.289 Chirality : 0.044 0.110 178 Planarity : 0.002 0.018 206 Dihedral : 4.111 17.526 160 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.73 % Allowed : 25.37 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.63), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.001 0.000 PHE F 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1090.63 seconds wall clock time: 19 minutes 55.89 seconds (1195.89 seconds total)