Starting phenix.real_space_refine on Wed Mar 5 14:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_19849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_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/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_19849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_19849.map" model { file = "/net/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_19849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo9_19849/03_2025/9eo9_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. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1190 Number of models: 1 Model: "" Number of chains: 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: 3.56, per 1000 atoms: 2.99 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 - 3.00 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: 0.28 Conformation dependent library (CDL) restraints added in 304.0 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: 0.49 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: 0.35 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: 0.00 - 1.64: 1258 1.64 - 3.29: 275 3.29 - 4.93: 68 4.93 - 6.58: 13 6.58 - 8.22: 6 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: 0.01 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 11.300 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.1790 time to fit residues: 5.8860 Evaluate side-chains 20 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.315625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.280340 restraints weight = 7383.350| |-----------------------------------------------------------------------------| r_work (start): 0.5120 rms_B_bonded: 6.75 r_work: 0.5158 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.5158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4926 r_free = 0.4926 target_work(ls_wunit_k1) = 0.288 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4926 r_free = 0.4926 target_work(ls_wunit_k1) = 0.287 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 2.52 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 to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.124 Fit side-chains REVERT: B 336 GLN cc_start: 0.6168 (mt0) cc_final: 0.5563 (mm110) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1525 time to fit residues: 3.9329 Evaluate side-chains 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 1 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.5107 r_free = 0.5107 target = 0.309754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5249 r_free = 0.5249 target = 0.270698 restraints weight = 9816.588| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 7.37 r_work: 0.5098 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4896 r_free = 0.4896 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4896 r_free = 0.4896 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1210 Z= 0.165 Angle : 0.723 7.584 1620 Z= 0.342 Chirality : 0.050 0.128 180 Planarity : 0.002 0.012 208 Dihedral : 6.682 42.702 164 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.41 % Allowed : 11.03 % Favored : 84.56 % 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 (0.47), 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 0.003 0.001 HIS B 330 PHE 0.009 0.002 PHE B 346 TYR 0.019 0.003 TYR B 310 ARG 0.002 0.000 ARG A 349 *********************** 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 27 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.143 Fit side-chains REVERT: A 349 ARG cc_start: 0.5433 (mmp-170) cc_final: 0.4494 (ptt90) REVERT: B 336 GLN cc_start: 0.5872 (mt0) cc_final: 0.5560 (mm110) REVERT: B 370 LYS cc_start: 0.7948 (tttt) cc_final: 0.7449 (mttt) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.2173 time to fit residues: 5.6849 Evaluate side-chains 22 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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: 0.0980 chunk 4 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.4204 ------------------------------------------------------------------------------- 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 = 0.5109 r_free = 0.5109 target = 0.310307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.272854 restraints weight = 6216.209| |-----------------------------------------------------------------------------| r_work (start): 0.5056 rms_B_bonded: 7.43 r_work: 0.5147 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work (final): 0.5147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4940 r_free = 0.4940 target_work(ls_wunit_k1) = 0.306 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4940 r_free = 0.4940 target_work(ls_wunit_k1) = 0.306 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1210 Z= 0.154 Angle : 0.707 7.863 1620 Z= 0.325 Chirality : 0.049 0.126 180 Planarity : 0.002 0.010 208 Dihedral : 5.863 23.591 164 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 12.50 % Favored : 84.56 % 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 0.007 0.001 PHE A 378 TYR 0.009 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 24 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.136 Fit side-chains REVERT: B 336 GLN cc_start: 0.5732 (mt0) cc_final: 0.5495 (mm110) REVERT: B 345 ASP cc_start: 0.8391 (p0) cc_final: 0.7883 (p0) REVERT: B 370 LYS cc_start: 0.7763 (tttt) cc_final: 0.7382 (mttt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1986 time to fit residues: 4.8048 Evaluate side-chains 22 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 2 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.302334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.265434 restraints weight = 9470.843| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 6.67 r_work: 0.5085 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4931 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4791 r_free = 0.4791 target_work(ls_wunit_k1) = 0.272 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4791 r_free = 0.4791 target_work(ls_wunit_k1) = 0.272 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 1210 Z= 0.340 Angle : 0.864 7.559 1620 Z= 0.419 Chirality : 0.054 0.133 180 Planarity : 0.004 0.027 208 Dihedral : 6.963 30.775 164 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.94 % Allowed : 13.97 % Favored : 83.09 % 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: -2.78 (0.51), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 330 PHE 0.017 0.003 PHE A 378 TYR 0.020 0.005 TYR A 310 ARG 0.002 0.001 ARG B 349 *********************** 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 22 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.136 Fit side-chains REVERT: B 336 GLN cc_start: 0.6052 (mt0) cc_final: 0.5597 (mm110) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.2091 time to fit residues: 4.5962 Evaluate side-chains 21 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.5072 r_free = 0.5072 target = 0.306930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.271444 restraints weight = 6815.379| |-----------------------------------------------------------------------------| r_work (start): 0.5032 rms_B_bonded: 7.02 r_work: 0.5109 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work (final): 0.5109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4894 r_free = 0.4894 target_work(ls_wunit_k1) = 0.285 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4894 r_free = 0.4894 target_work(ls_wunit_k1) = 0.285 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1210 Z= 0.193 Angle : 0.755 7.900 1620 Z= 0.356 Chirality : 0.050 0.127 180 Planarity : 0.002 0.013 208 Dihedral : 6.310 26.397 164 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.21 % Allowed : 13.97 % 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: -2.63 (0.54), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 330 PHE 0.008 0.001 PHE A 378 TYR 0.016 0.004 TYR B 310 ARG 0.002 0.000 ARG A 379 *********************** 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 22 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.128 Fit side-chains REVERT: A 349 ARG cc_start: 0.5437 (mmp-170) cc_final: 0.4400 (ptm-80) REVERT: B 336 GLN cc_start: 0.5926 (mt0) cc_final: 0.5647 (mm110) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.2473 time to fit residues: 5.3577 Evaluate side-chains 16 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.5101 r_free = 0.5101 target = 0.309614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.276533 restraints weight = 6677.879| |-----------------------------------------------------------------------------| r_work (start): 0.5068 rms_B_bonded: 6.96 r_work: 0.5129 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.5129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4910 r_free = 0.4910 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4910 r_free = 0.4910 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1210 Z= 0.156 Angle : 0.744 7.972 1620 Z= 0.349 Chirality : 0.048 0.126 180 Planarity : 0.003 0.029 208 Dihedral : 5.882 28.047 164 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.21 % Allowed : 14.71 % Favored : 83.09 % 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: -2.51 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.007 0.001 PHE A 378 TYR 0.009 0.002 TYR A 310 ARG 0.008 0.001 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 19 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.141 Fit side-chains REVERT: A 349 ARG cc_start: 0.5461 (mmp-170) cc_final: 0.4413 (ptm-80) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1906 time to fit residues: 3.6259 Evaluate side-chains 14 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 0.0670 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 3 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8618 ------------------------------------------------------------------------------- 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 = 0.5141 r_free = 0.5141 target = 0.314292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5252 r_free = 0.5252 target = 0.283438 restraints weight = 7914.678| |-----------------------------------------------------------------------------| r_work (start): 0.5104 rms_B_bonded: 7.05 r_work: 0.5163 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4957 r_free = 0.4957 target_work(ls_wunit_k1) = 0.305 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4957 r_free = 0.4957 target_work(ls_wunit_k1) = 0.305 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 1210 Z= 0.124 Angle : 0.785 10.860 1620 Z= 0.365 Chirality : 0.047 0.123 180 Planarity : 0.003 0.028 208 Dihedral : 5.507 33.118 164 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 15.44 % 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: -2.41 (0.56), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.002 0.001 PHE A 378 TYR 0.018 0.003 TYR B 310 ARG 0.007 0.001 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 18 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.127 Fit side-chains REVERT: A 349 ARG cc_start: 0.5313 (mmp-170) cc_final: 0.4351 (ptm-80) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1409 time to fit residues: 2.6102 Evaluate side-chains 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 overall best weight: 1.6744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.312350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.281298 restraints weight = 7626.308| |-----------------------------------------------------------------------------| r_work (start): 0.5094 rms_B_bonded: 6.49 r_work: 0.5161 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.5161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4433 r_free = 0.4433 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4431 r_free = 0.4431 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1210 Z= 0.143 Angle : 0.779 10.097 1620 Z= 0.361 Chirality : 0.047 0.124 180 Planarity : 0.003 0.025 208 Dihedral : 5.323 27.446 164 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.21 % Allowed : 16.18 % 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: -2.42 (0.56), 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 0.002 0.001 HIS B 330 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.007 0.001 ARG A 379 *********************** 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 15 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.143 Fit side-chains REVERT: A 349 ARG cc_start: 0.5406 (mmp-170) cc_final: 0.4379 (ptm-80) outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.1385 time to fit residues: 2.1608 Evaluate side-chains 14 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 0.0020 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0020 chunk 5 optimal weight: 6.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 = 0.5135 r_free = 0.5135 target = 0.313747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.283867 restraints weight = 5934.474| |-----------------------------------------------------------------------------| r_work (start): 0.5097 rms_B_bonded: 6.77 r_work: 0.5146 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.5146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4950 r_free = 0.4950 target_work(ls_wunit_k1) = 0.306 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4952 r_free = 0.4952 target_work(ls_wunit_k1) = 0.305 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 1210 Z= 0.130 Angle : 0.766 9.969 1620 Z= 0.354 Chirality : 0.047 0.123 180 Planarity : 0.003 0.024 208 Dihedral : 5.220 29.345 164 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 16.18 % 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: -2.39 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 330 PHE 0.003 0.001 PHE A 378 TYR 0.016 0.003 TYR B 310 ARG 0.007 0.001 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 15 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.135 Fit side-chains REVERT: A 349 ARG cc_start: 0.5357 (mmp-170) cc_final: 0.4344 (ptm-80) outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.1339 time to fit residues: 2.0904 Evaluate side-chains 15 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 0.0070 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 5 optimal weight: 8.9990 overall best weight: 2.1640 ------------------------------------------------------------------------------- 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 = 0.5120 r_free = 0.5120 target = 0.311799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.281034 restraints weight = 9309.547| |-----------------------------------------------------------------------------| r_work (start): 0.5081 rms_B_bonded: 6.82 r_work: 0.5138 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.5138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4929 r_free = 0.4929 target_work(ls_wunit_k1) = 0.286 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4929 r_free = 0.4929 target_work(ls_wunit_k1) = 0.286 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1210 Z= 0.159 Angle : 0.778 9.645 1620 Z= 0.361 Chirality : 0.048 0.125 180 Planarity : 0.003 0.024 208 Dihedral : 5.327 26.965 164 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.21 % Allowed : 16.18 % 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: -2.39 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.007 0.001 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.54 seconds wall clock time: 22 minutes 17.30 seconds (1337.30 seconds total)