Starting phenix.real_space_refine on Mon Feb 10 19:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vhl_21207/02_2025/6vhl_21207_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vhl_21207/02_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_21207/02_2025/6vhl_21207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vhl_21207/02_2025/6vhl_21207.map" model { file = "/net/cci-nas-00/data/ceres_data/6vhl_21207/02_2025/6vhl_21207_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vhl_21207/02_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-5592/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: 1.08, per 1000 atoms: 0.91 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: 0.72 Conformation dependent library (CDL) restraints added in 939.1 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: 0.46 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: 0.76 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: 0.820 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: 0.000 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- 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 : 0.132 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: 0.2396 time to fit residues: 11.6924 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 : 0.148 ------------------------------------------------------------------------------- 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 : 0.140 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: 0.2165 time to fit residues: 9.9213 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 : 0.130 ------------------------------------------------------------------------------- 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 : 0.159 Fit side-chains REVERT: E 311 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8262 (mmtt) REVERT: E 349 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.6455 (mmp-170) REVERT: F 340 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8062 (mmtm) REVERT: F 349 ARG cc_start: 0.5497 (ptt-90) cc_final: 0.4774 (mmp-170) REVERT: F 375 LYS cc_start: 0.8552 (mttt) cc_final: 0.8316 (pptt) outliers start: 8 outliers final: 2 residues processed: 50 average time/residue: 0.1872 time to fit residues: 10.0631 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 : 0.133 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.139294 restraints weight = 2957.883| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 4.30 r_work: 0.4289 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1206 Z= 0.108 Angle : 0.592 6.558 1608 Z= 0.286 Chirality : 0.045 0.114 178 Planarity : 0.004 0.034 206 Dihedral : 6.023 44.055 164 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 0.001 0.001 TYR E 310 ARG 0.001 0.000 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 : 0.153 Fit side-chains REVERT: E 311 LYS cc_start: 0.8841 (ttpp) cc_final: 0.8361 (mmtt) REVERT: E 349 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.6517 (mmp-170) REVERT: F 311 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8433 (mmtt) REVERT: F 340 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8102 (mmtm) REVERT: F 349 ARG cc_start: 0.5464 (ptt-90) cc_final: 0.4711 (mmp-170) REVERT: F 351 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: F 372 GLU cc_start: 0.7608 (mp0) cc_final: 0.7400 (mp0) REVERT: F 375 LYS cc_start: 0.8587 (mttt) cc_final: 0.8306 (pptt) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.2072 time to fit residues: 10.6338 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 : 0.160 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 6 optimal weight: 0.0370 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.153829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.143546 restraints weight = 2896.393| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 4.29 r_work: 0.4337 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.6518 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= 0.091 Angle : 0.577 5.903 1608 Z= 0.271 Chirality : 0.045 0.114 178 Planarity : 0.004 0.034 206 Dihedral : 4.463 17.520 160 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.99 % Allowed : 24.63 % 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: -3.68 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 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 43 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.154 Fit side-chains REVERT: E 311 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8333 (mmtt) REVERT: E 349 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.6492 (mmp-170) REVERT: E 378 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6196 (t80) REVERT: F 311 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8399 (mmtt) REVERT: F 340 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8262 (mmtm) REVERT: F 349 ARG cc_start: 0.5361 (ptt-90) cc_final: 0.4780 (mmp-170) REVERT: F 351 GLN cc_start: 0.8771 (pt0) cc_final: 0.8456 (pt0) REVERT: F 375 LYS cc_start: 0.8593 (mttt) cc_final: 0.8193 (pptt) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.2164 time to fit residues: 9.5101 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 : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER 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: 0.0970 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.152201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.141949 restraints weight = 2851.913| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 4.29 r_work: 0.4310 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.6764 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 : 0.572 5.924 1608 Z= 0.272 Chirality : 0.044 0.112 178 Planarity : 0.003 0.028 206 Dihedral : 4.261 17.034 160 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.73 % Allowed : 22.39 % 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 (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: -3.48 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.001 0.000 PHE F 346 TYR 0.001 0.000 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** 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 41 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.142 Fit side-chains REVERT: E 311 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8325 (mmtt) REVERT: E 349 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.6528 (mmp-170) REVERT: E 378 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6702 (t80) REVERT: F 311 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8396 (mmtt) REVERT: F 340 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8201 (pttm) REVERT: F 349 ARG cc_start: 0.5563 (ptt-90) cc_final: 0.4995 (mmp-170) REVERT: F 375 LYS cc_start: 0.8634 (mttt) cc_final: 0.8212 (pptt) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.2096 time to fit residues: 8.7607 Evaluate side-chains 41 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 368 ASN 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 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.153584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.143300 restraints weight = 2898.212| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 4.29 r_work: 0.4330 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1206 Z= 0.095 Angle : 0.586 6.456 1608 Z= 0.268 Chirality : 0.044 0.112 178 Planarity : 0.003 0.021 206 Dihedral : 4.143 17.237 160 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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: -3.33 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (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 346 TYR 0.001 0.000 TYR E 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 40 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.167 Fit side-chains REVERT: E 311 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8336 (mmtt) REVERT: E 349 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.6522 (mmp-170) REVERT: F 311 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8392 (mmtt) REVERT: F 340 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8164 (pttm) REVERT: F 343 LYS cc_start: 0.5148 (tppt) cc_final: 0.4858 (tppt) REVERT: F 349 ARG cc_start: 0.5483 (ptt-90) cc_final: 0.4988 (mmp-170) REVERT: F 375 LYS cc_start: 0.8628 (mttt) cc_final: 0.8193 (pptt) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.2213 time to fit residues: 9.0138 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 : 0.149 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.150655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.140278 restraints weight = 2973.536| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 4.28 r_work: 0.4301 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.003 0.020 1206 Z= 0.120 Angle : 0.583 5.866 1608 Z= 0.274 Chirality : 0.044 0.111 178 Planarity : 0.003 0.021 206 Dihedral : 4.474 16.931 160 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.73 % Allowed : 24.63 % Favored : 71.64 % 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: -3.27 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.002 0.000 PHE E 378 TYR 0.001 0.000 TYR E 310 ARG 0.001 0.000 ARG F 379 *********************** 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 38 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.146 Fit side-chains REVERT: E 311 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8340 (mmtt) REVERT: E 349 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.6478 (mmp-170) REVERT: F 311 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8445 (mmtt) REVERT: F 349 ARG cc_start: 0.5527 (ptt-90) cc_final: 0.4894 (mmp-170) REVERT: F 358 ASP cc_start: 0.8562 (p0) cc_final: 0.7641 (m-30) REVERT: F 375 LYS cc_start: 0.8645 (mttt) cc_final: 0.8203 (pptt) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.2143 time to fit residues: 8.4935 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 : 0.136 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.0170 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.151661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.141304 restraints weight = 2928.105| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 4.20 r_work: 0.4290 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.7554 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= 0.128 Angle : 0.642 5.736 1608 Z= 0.305 Chirality : 0.044 0.111 178 Planarity : 0.003 0.021 206 Dihedral : 4.400 17.073 160 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % 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: -3.19 (0.62), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.002 0.000 PHE E 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** 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 39 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.200 Fit side-chains REVERT: E 311 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8353 (mmtt) REVERT: E 349 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.6459 (mmp-170) REVERT: F 311 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8423 (mmtt) REVERT: F 343 LYS cc_start: 0.4974 (tppt) cc_final: 0.4585 (tppt) REVERT: F 349 ARG cc_start: 0.5681 (ptt-90) cc_final: 0.5013 (mmp-170) REVERT: F 358 ASP cc_start: 0.8534 (p0) cc_final: 0.7545 (m-30) REVERT: F 375 LYS cc_start: 0.8601 (mttt) cc_final: 0.8240 (pptt) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.2141 time to fit residues: 8.9674 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 : 0.130 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 chunk 4 optimal weight: 0.0020 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.0030 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.152991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.142357 restraints weight = 2835.048| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 4.26 r_work: 0.4339 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.7841 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= 0.107 Angle : 0.625 5.876 1608 Z= 0.295 Chirality : 0.044 0.112 178 Planarity : 0.003 0.021 206 Dihedral : 4.047 17.010 160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.90 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: -3.05 (0.63), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.002 0.000 PHE F 346 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 ********************** 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 40 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.145 Fit side-chains REVERT: E 311 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8366 (mmtt) REVERT: E 349 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.6456 (mmp-170) REVERT: F 311 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8411 (mmtt) REVERT: F 338 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7935 (tm-30) REVERT: F 343 LYS cc_start: 0.4947 (tppt) cc_final: 0.4670 (tppt) REVERT: F 349 ARG cc_start: 0.5753 (ptt-90) cc_final: 0.5115 (mmp-170) REVERT: F 358 ASP cc_start: 0.8356 (p0) cc_final: 0.7364 (m-30) REVERT: F 375 LYS cc_start: 0.8629 (mttt) cc_final: 0.8198 (pptt) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1982 time to fit residues: 8.3181 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.149853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.139149 restraints weight = 2917.996| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 4.16 r_work: 0.4292 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.7765 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= 0.146 Angle : 0.642 5.863 1608 Z= 0.309 Chirality : 0.044 0.111 178 Planarity : 0.003 0.017 206 Dihedral : 4.364 16.053 160 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -3.04 (0.64), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.49), 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 346 TYR 0.002 0.001 TYR E 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: 1106.10 seconds wall clock time: 20 minutes 53.82 seconds (1253.82 seconds total)