Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo9_19849/08_2024/9eo9_19849_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= 0.002 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 4 5.16 5 C 744 2.51 5 N 218 2.21 5 O 224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 1190 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} bond proxies already assigned to first conformer: 588 Chain: "B" Number of atoms: 595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} bond proxies already assigned to first conformer: 588 Residues with excluded nonbonded symmetry interactions: 2 residue group: pdb=" N AMET A 337 " occ=0.50 ... (13 atoms not shown) pdb=" CG2BVAL A 337 " occ=0.50 residue group: pdb=" N AMET B 337 " occ=0.50 ... (13 atoms not shown) pdb=" CG2BVAL B 337 " occ=0.50 Time building chain proxies: 1.79, per 1000 atoms: 1.50 Number of scatterers: 1190 At special positions: 0 Unit cell: (91.464, 133.488, 27.192, 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 4 16.00 O 224 8.00 N 218 7.00 C 744 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 - 3.50 Amino acid : False - 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: 1.53 Conformation dependent library (CDL) restraints added in 476.7 milliseconds 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 276 1.33 - 1.46: 315 1.46 - 1.58: 612 1.58 - 1.70: 0 1.70 - 1.83: 7 Bond restraints: 1210 Sorted by residual: bond pdb=" C GLN B 336 " pdb=" N BVAL B 337 " ideal model delta sigma weight residual 1.330 1.791 -0.460 1.26e-02 6.30e+03 1.33e+03 bond pdb=" C BVAL B 337 " pdb=" N GLU B 338 " ideal model delta sigma weight residual 1.330 1.470 -0.140 1.44e-02 4.82e+03 9.40e+01 bond pdb=" C GLN A 336 " pdb=" N BVAL A 337 " ideal model delta sigma weight residual 1.331 1.407 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.319 0.035 1.10e-02 8.26e+03 9.87e+00 bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.15e+00 ... (remaining 1205 not shown) Histogram of bond angle deviations from ideal: 100.96 - 107.04: 45 107.04 - 113.12: 593 113.12 - 119.20: 411 119.20 - 125.28: 546 125.28 - 131.36: 25 Bond angle restraints: 1620 Sorted by residual: angle pdb=" O GLN B 336 " pdb=" C GLN B 336 " pdb=" N BVAL B 337 " ideal model delta sigma weight residual 123.14 131.36 -8.22 1.30e+00 5.92e-01 4.00e+01 angle pdb=" O BVAL B 337 " pdb=" C BVAL B 337 " pdb=" N GLU B 338 " ideal model delta sigma weight residual 123.18 116.67 6.51 1.05e+00 9.07e-01 3.85e+01 angle pdb=" CA GLN B 336 " pdb=" C GLN B 336 " pdb=" N BVAL B 337 " ideal model delta sigma weight residual 116.57 108.46 8.11 1.40e+00 5.10e-01 3.36e+01 angle pdb=" CA THR B 361 " pdb=" CB THR B 361 " pdb=" OG1 THR B 361 " ideal model delta sigma weight residual 109.60 101.41 8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" CA ASP A 314 " pdb=" CB ASP A 314 " pdb=" CG ASP A 314 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.23e+01 ... (remaining 1615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 653 16.68 - 33.35: 74 33.35 - 50.03: 10 50.03 - 66.71: 1 66.71 - 83.38: 2 Dihedral angle restraints: 740 sinusoidal: 310 harmonic: 430 Sorted by residual: dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual -180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA VAL B 318 " pdb=" C VAL B 318 " pdb=" N THR B 319 " pdb=" CA THR B 319 " ideal model delta harmonic sigma weight residual 180.00 -148.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual 180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 737 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.068: 85 0.068 - 0.136: 72 0.136 - 0.204: 18 0.204 - 0.271: 3 0.271 - 0.339: 2 Chirality restraints: 180 Sorted by residual: chirality pdb=" CA ASN B 327 " pdb=" N ASN B 327 " pdb=" C ASN B 327 " pdb=" CB ASN B 327 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA LYS B 317 " pdb=" N LYS B 317 " pdb=" C LYS B 317 " pdb=" CB LYS B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ASP B 348 " pdb=" N ASP B 348 " pdb=" C ASP B 348 " pdb=" CB ASP B 348 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 177 not shown) Planarity restraints: 208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BVAL B 337 " 0.026 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C BVAL B 337 " -0.083 2.00e-02 2.50e+03 pdb=" O BVAL B 337 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU B 338 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 363 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C VAL A 363 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL A 363 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 364 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 336 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C GLN B 336 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 336 " -0.015 2.00e-02 2.50e+03 pdb=" N BVAL B 337 " -0.010 2.00e-02 2.50e+03 ... (remaining 205 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 672 3.09 - 3.54: 980 3.54 - 4.00: 1336 4.00 - 4.45: 1120 4.45 - 4.90: 1942 Nonbonded interactions: 6050 Sorted by model distance: nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.638 3.040 nonbonded pdb=" N LYS B 347 " pdb=" O LYS B 347 " model vdw 2.674 2.496 nonbonded pdb=" N LYS A 321 " pdb=" O LYS A 321 " model vdw 2.674 2.496 nonbonded pdb=" O LYS A 311 " pdb=" CA PRO A 312 " model vdw 2.677 2.776 nonbonded pdb=" O LYS B 311 " pdb=" CA PRO B 312 " model vdw 2.678 2.776 ... (remaining 6045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 304 through 336 or resid 338 through 380)) selection = (chain 'B' and (resid 304 through 336 or resid 338 through 380)) } 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=0.50 max=1.00 mean=0.99 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: 3.320 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 11.070 Find NCS groups from input model: 0.050 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.016 0.460 1210 Z= 1.220 Angle : 1.575 8.219 1620 Z= 1.017 Chirality : 0.097 0.339 180 Planarity : 0.011 0.059 208 Dihedral : 14.488 83.382 468 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.88 % Allowed : 8.09 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.00 % 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: -4.62 (0.38), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.29), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 374 PHE 0.016 0.005 PHE B 346 TYR 0.020 0.009 TYR B 310 ARG 0.014 0.003 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.143 Fit side-chains REVERT: A 336 GLN cc_start: 0.8021 (mt0) cc_final: 0.7507 (mm-40) REVERT: A 349 ARG cc_start: 0.8115 (mtt180) cc_final: 0.6928 (mmp-170) REVERT: B 311 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8333 (tttm) REVERT: B 338 GLU cc_start: 0.8082 (tt0) cc_final: 0.6978 (pm20) REVERT: B 340 LYS cc_start: 0.7001 (mttt) cc_final: 0.6210 (mmmt) REVERT: B 347 LYS cc_start: 0.8053 (mttt) cc_final: 0.7709 (mptt) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.1789 time to fit residues: 5.8669 Evaluate side-chains 20 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1210 Z= 0.139 Angle : 0.662 6.450 1620 Z= 0.325 Chirality : 0.050 0.130 180 Planarity : 0.003 0.016 208 Dihedral : 7.626 55.337 167 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.21 % Allowed : 11.76 % Favored : 86.03 % 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: -3.34 (0.42), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.32), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.005 0.001 PHE B 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.141 Fit side-chains REVERT: A 336 GLN cc_start: 0.8136 (mt0) cc_final: 0.7577 (mm-40) REVERT: A 349 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7177 (mmp-170) REVERT: B 311 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8532 (tttm) REVERT: B 336 GLN cc_start: 0.6562 (mt0) cc_final: 0.5343 (mm110) REVERT: B 338 GLU cc_start: 0.7987 (tt0) cc_final: 0.6964 (pm20) REVERT: B 340 LYS cc_start: 0.6997 (mttt) cc_final: 0.6296 (mmmt) REVERT: B 347 LYS cc_start: 0.7972 (mttt) cc_final: 0.7663 (mmtm) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1610 time to fit residues: 4.1570 Evaluate side-chains 19 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS A 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1210 Z= 0.220 Angle : 0.711 7.310 1620 Z= 0.343 Chirality : 0.051 0.130 180 Planarity : 0.003 0.016 208 Dihedral : 6.533 26.699 164 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 13.24 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.79 (0.48), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.36), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.010 0.002 PHE A 378 TYR 0.019 0.004 TYR B 310 ARG 0.002 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.142 Fit side-chains REVERT: A 336 GLN cc_start: 0.8107 (mt0) cc_final: 0.7608 (mm-40) REVERT: A 349 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7298 (mmp-170) REVERT: B 311 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8537 (tttm) REVERT: B 336 GLN cc_start: 0.6379 (mt0) cc_final: 0.5315 (mm110) REVERT: B 338 GLU cc_start: 0.7899 (tt0) cc_final: 0.6810 (pm20) REVERT: B 340 LYS cc_start: 0.7252 (mttt) cc_final: 0.6590 (mmmt) REVERT: B 347 LYS cc_start: 0.7887 (mttt) cc_final: 0.7612 (mmtp) REVERT: B 351 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7567 (tm-30) REVERT: B 353 LYS cc_start: 0.8506 (mtpt) cc_final: 0.7956 (tttt) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.2162 time to fit residues: 6.0904 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.0020 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1210 Z= 0.162 Angle : 0.670 7.745 1620 Z= 0.311 Chirality : 0.049 0.128 180 Planarity : 0.002 0.012 208 Dihedral : 5.983 27.426 164 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.68 % Allowed : 13.97 % Favored : 82.35 % 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: -2.47 (0.51), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.008 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.143 Fit side-chains REVERT: A 336 GLN cc_start: 0.8085 (mt0) cc_final: 0.7633 (mm-40) REVERT: A 349 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7228 (mmp-170) REVERT: A 379 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7886 (ttm110) REVERT: B 311 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8534 (tttm) REVERT: B 336 GLN cc_start: 0.6246 (mt0) cc_final: 0.5262 (mm110) REVERT: B 338 GLU cc_start: 0.7877 (tt0) cc_final: 0.6806 (pm20) REVERT: B 340 LYS cc_start: 0.7205 (mttt) cc_final: 0.6518 (mmmt) REVERT: B 347 LYS cc_start: 0.7834 (mttt) cc_final: 0.7547 (mmtp) REVERT: B 353 LYS cc_start: 0.8516 (mtpt) cc_final: 0.7989 (tttt) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.2164 time to fit residues: 5.4125 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1210 Z= 0.134 Angle : 0.635 7.587 1620 Z= 0.293 Chirality : 0.048 0.126 180 Planarity : 0.002 0.009 208 Dihedral : 5.623 27.807 164 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: -2.25 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.020 0.004 TYR B 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.144 Fit side-chains REVERT: A 336 GLN cc_start: 0.8092 (mt0) cc_final: 0.7617 (mm-40) REVERT: A 349 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7211 (mmp-170) REVERT: A 379 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7876 (ttm110) REVERT: B 311 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8545 (tttm) REVERT: B 336 GLN cc_start: 0.6176 (mt0) cc_final: 0.5380 (mm110) REVERT: B 338 GLU cc_start: 0.7860 (tt0) cc_final: 0.6849 (pm20) REVERT: B 340 LYS cc_start: 0.7180 (mttt) cc_final: 0.6522 (mmmt) REVERT: B 347 LYS cc_start: 0.7817 (mttt) cc_final: 0.7595 (mmtm) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.2249 time to fit residues: 5.3985 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1210 Z= 0.204 Angle : 0.697 7.793 1620 Z= 0.329 Chirality : 0.049 0.127 180 Planarity : 0.002 0.016 208 Dihedral : 5.894 25.373 164 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 15.44 % Favored : 81.62 % 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: -2.33 (0.56), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.010 0.002 PHE A 378 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.147 Fit side-chains REVERT: A 336 GLN cc_start: 0.8062 (mt0) cc_final: 0.7561 (mm-40) REVERT: A 349 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7153 (mmp-170) REVERT: A 379 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7866 (ttm110) REVERT: B 311 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8557 (tttm) REVERT: B 336 GLN cc_start: 0.6317 (mt0) cc_final: 0.5395 (mm110) REVERT: B 338 GLU cc_start: 0.7799 (tt0) cc_final: 0.6769 (pm20) REVERT: B 340 LYS cc_start: 0.7284 (mttt) cc_final: 0.6801 (mmpt) REVERT: B 347 LYS cc_start: 0.7751 (mttt) cc_final: 0.7484 (mmtp) REVERT: B 351 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7260 (tm-30) REVERT: B 353 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7745 (tttt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.2090 time to fit residues: 5.2115 Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1210 Z= 0.202 Angle : 0.691 7.911 1620 Z= 0.327 Chirality : 0.049 0.128 180 Planarity : 0.003 0.016 208 Dihedral : 5.879 26.427 164 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: -2.42 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.010 0.002 PHE A 378 TYR 0.021 0.004 TYR B 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.149 Fit side-chains REVERT: A 336 GLN cc_start: 0.8102 (mt0) cc_final: 0.7645 (mm-40) REVERT: A 349 ARG cc_start: 0.8046 (mtt180) cc_final: 0.6750 (ptt90) REVERT: A 379 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7893 (ttm110) REVERT: B 311 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8565 (tttm) REVERT: B 336 GLN cc_start: 0.6296 (mt0) cc_final: 0.5318 (mm110) REVERT: B 338 GLU cc_start: 0.7825 (tt0) cc_final: 0.6764 (pm20) REVERT: B 340 LYS cc_start: 0.7277 (mttt) cc_final: 0.6686 (mmmt) REVERT: B 347 LYS cc_start: 0.7757 (mttt) cc_final: 0.7510 (mmtp) REVERT: B 351 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 353 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7712 (tttt) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.2163 time to fit residues: 5.6591 Evaluate side-chains 25 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1210 Z= 0.112 Angle : 0.643 8.204 1620 Z= 0.295 Chirality : 0.047 0.125 180 Planarity : 0.002 0.010 208 Dihedral : 5.367 28.710 164 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: -2.23 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.128 Fit side-chains REVERT: A 336 GLN cc_start: 0.8119 (mt0) cc_final: 0.7585 (mm-40) REVERT: A 349 ARG cc_start: 0.7988 (mtt180) cc_final: 0.6718 (ptt90) REVERT: A 379 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7876 (ttm110) REVERT: B 311 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8562 (tttm) REVERT: B 336 GLN cc_start: 0.6142 (mt0) cc_final: 0.5399 (mm110) REVERT: B 338 GLU cc_start: 0.7829 (tt0) cc_final: 0.6830 (pm20) REVERT: B 340 LYS cc_start: 0.7202 (mttt) cc_final: 0.6642 (mmmt) REVERT: B 351 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 353 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7749 (tttt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.2133 time to fit residues: 5.3456 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.0980 chunk 12 optimal weight: 0.0040 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1210 Z= 0.141 Angle : 0.710 8.547 1620 Z= 0.328 Chirality : 0.047 0.125 180 Planarity : 0.002 0.013 208 Dihedral : 5.368 25.979 164 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.94 % Allowed : 15.44 % Favored : 81.62 % 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: -2.33 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.021 0.004 TYR B 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.146 Fit side-chains REVERT: A 336 GLN cc_start: 0.8152 (mt0) cc_final: 0.7588 (mm-40) REVERT: A 349 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6706 (ptt90) REVERT: A 379 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7966 (ttm110) REVERT: B 311 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8592 (tttm) REVERT: B 336 GLN cc_start: 0.6141 (mt0) cc_final: 0.5420 (mm110) REVERT: B 338 GLU cc_start: 0.7831 (tt0) cc_final: 0.6789 (pm20) REVERT: B 340 LYS cc_start: 0.7252 (mttt) cc_final: 0.6700 (mmmt) REVERT: B 351 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 353 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7809 (tttt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.2338 time to fit residues: 5.6092 Evaluate side-chains 22 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1210 Z= 0.237 Angle : 0.801 9.257 1620 Z= 0.380 Chirality : 0.050 0.127 180 Planarity : 0.003 0.020 208 Dihedral : 5.870 24.733 164 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % Favored : 80.88 % 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: -2.53 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 330 PHE 0.012 0.002 PHE A 378 TYR 0.015 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.143 Fit side-chains REVERT: A 336 GLN cc_start: 0.8135 (mt0) cc_final: 0.7616 (mm-40) REVERT: A 349 ARG cc_start: 0.7968 (mtt180) cc_final: 0.6650 (ptt90) REVERT: B 311 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8557 (tttm) REVERT: B 336 GLN cc_start: 0.6308 (mt0) cc_final: 0.5422 (mm110) REVERT: B 338 GLU cc_start: 0.7762 (tt0) cc_final: 0.6751 (pm20) REVERT: B 340 LYS cc_start: 0.7303 (mttt) cc_final: 0.6726 (mmmt) REVERT: B 351 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 353 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7879 (tttt) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.2136 time to fit residues: 4.9172 Evaluate side-chains 22 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.312005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.277085 restraints weight = 9479.431| |-----------------------------------------------------------------------------| r_work (start): 0.5080 rms_B_bonded: 7.25 r_work: 0.5118 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.5118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4900 r_free = 0.4900 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4900 r_free = 0.4900 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1210 Z= 0.125 Angle : 0.727 8.875 1620 Z= 0.333 Chirality : 0.047 0.125 180 Planarity : 0.002 0.011 208 Dihedral : 5.521 26.913 164 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.21 % Allowed : 16.91 % Favored : 80.88 % 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: -2.43 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.005 0.001 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 876.30 seconds wall clock time: 15 minutes 58.78 seconds (958.78 seconds total)