Starting phenix.real_space_refine on Mon Jan 13 12:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo9_19849/01_2025/9eo9_19849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo9_19849/01_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_19849/01_2025/9eo9_19849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo9_19849/01_2025/9eo9_19849.map" model { file = "/net/cci-nas-00/data/ceres_data/9eo9_19849/01_2025/9eo9_19849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo9_19849/01_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-5571/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: 3.61, per 1000 atoms: 3.03 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: 0.27 Conformation dependent library (CDL) restraints added in 301.7 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: 0.59 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: 0.33 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.810 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- 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 : 0.153 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: 0.1834 time to fit residues: 6.0269 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 : 0.143 ------------------------------------------------------------------------------- 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 : 0.133 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: 0.1554 time to fit residues: 4.0097 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 : 0.132 ------------------------------------------------------------------------------- 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 = 9816.587| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 7.37 r_work: 0.5095 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 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 = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.190 Fit side-chains REVERT: A 349 ARG cc_start: 0.5439 (mmp-170) cc_final: 0.4498 (ptt90) REVERT: B 336 GLN cc_start: 0.5867 (mt0) cc_final: 0.5554 (mm110) REVERT: B 370 LYS cc_start: 0.7968 (tttt) cc_final: 0.7458 (mttt) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.2440 time to fit residues: 6.3372 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 : 0.147 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.0570 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.9104 ------------------------------------------------------------------------------- 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 = 0.5098 r_free = 0.5098 target = 0.309275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.274350 restraints weight = 6081.043| |-----------------------------------------------------------------------------| r_work (start): 0.5054 rms_B_bonded: 7.12 r_work: 0.5125 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work (final): 0.5125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4913 r_free = 0.4913 target_work(ls_wunit_k1) = 0.286 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4913 r_free = 0.4913 target_work(ls_wunit_k1) = 0.286 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1210 Z= 0.177 Angle : 0.730 7.887 1620 Z= 0.338 Chirality : 0.049 0.126 180 Planarity : 0.002 0.013 208 Dihedral : 5.992 20.873 164 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.45 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: -2.51 (0.51), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (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 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: 0.5758 (mt0) cc_final: 0.5501 (mm110) REVERT: B 345 ASP cc_start: 0.8391 (p0) cc_final: 0.7883 (p0) REVERT: B 370 LYS cc_start: 0.7752 (tttt) cc_final: 0.7354 (mttt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.2031 time to fit residues: 4.8867 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 : 0.131 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.5061 r_free = 0.5061 target = 0.304478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.267513 restraints weight = 9987.287| |-----------------------------------------------------------------------------| r_work (start): 0.5006 rms_B_bonded: 6.75 r_work: 0.5080 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.5080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4866 r_free = 0.4866 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4866 r_free = 0.4866 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 1210 Z= 0.261 Angle : 0.798 7.655 1620 Z= 0.380 Chirality : 0.052 0.130 180 Planarity : 0.003 0.021 208 Dihedral : 6.537 26.080 164 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -2.66 (0.52), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 330 PHE 0.012 0.002 PHE A 378 TYR 0.016 0.004 TYR B 310 ARG 0.002 0.000 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 24 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.160 Fit side-chains REVERT: B 336 GLN cc_start: 0.5906 (mt0) cc_final: 0.5588 (mm110) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.2593 time to fit residues: 6.1690 Evaluate side-chains 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 1 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.5113 r_free = 0.5113 target = 0.311199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.278409 restraints weight = 6814.875| |-----------------------------------------------------------------------------| r_work (start): 0.5081 rms_B_bonded: 7.04 r_work: 0.5130 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.5130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1210 Z= 0.139 Angle : 0.721 7.959 1620 Z= 0.336 Chirality : 0.048 0.126 180 Planarity : 0.003 0.031 208 Dihedral : 5.912 28.930 164 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.14 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: -2.44 (0.54), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.008 0.001 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 18 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.142 Fit side-chains REVERT: A 349 ARG cc_start: 0.5460 (mmp-170) cc_final: 0.4453 (ptm-80) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1593 time to fit residues: 2.9454 Evaluate side-chains 16 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 12 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.9444 ------------------------------------------------------------------------------- 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 = 0.5101 r_free = 0.5101 target = 0.307732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.274128 restraints weight = 6724.085| |-----------------------------------------------------------------------------| r_work (start): 0.5067 rms_B_bonded: 6.81 r_work: 0.5117 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.5117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4910 r_free = 0.4910 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4912 r_free = 0.4912 target_work(ls_wunit_k1) = 0.283 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1210 Z= 0.182 Angle : 0.733 7.775 1620 Z= 0.345 Chirality : 0.049 0.126 180 Planarity : 0.003 0.024 208 Dihedral : 5.877 25.586 164 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -2.51 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.42), 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 0.018 0.004 TYR B 310 ARG 0.007 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 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.149 Fit side-chains REVERT: A 349 ARG cc_start: 0.5452 (mmp-170) cc_final: 0.4422 (ptm-80) outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1587 time to fit residues: 2.7683 Evaluate side-chains 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.5102 r_free = 0.5102 target = 0.307664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.274287 restraints weight = 7996.351| |-----------------------------------------------------------------------------| r_work (start): 0.5069 rms_B_bonded: 6.77 r_work: 0.5125 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.5125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4915 r_free = 0.4915 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 = 0.4915 r_free = 0.4915 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1210 Z= 0.188 Angle : 0.728 7.315 1620 Z= 0.346 Chirality : 0.049 0.126 180 Planarity : 0.003 0.022 208 Dihedral : 5.906 26.233 164 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -2.56 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 330 PHE 0.008 0.001 PHE A 378 TYR 0.011 0.002 TYR A 310 ARG 0.006 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: 3 poor density : 15 time to evaluate : 0.136 Fit side-chains REVERT: A 349 ARG cc_start: 0.5510 (mmp-170) cc_final: 0.4407 (ptm-80) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1549 time to fit residues: 2.8770 Evaluate side-chains 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 13 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.5077 r_free = 0.5077 target = 0.304923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.272053 restraints weight = 7760.669| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 6.68 r_work: 0.5132 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4977 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4831 r_free = 0.4831 target_work(ls_wunit_k1) = 0.274 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4831 r_free = 0.4831 target_work(ls_wunit_k1) = 0.274 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1210 Z= 0.245 Angle : 0.787 8.073 1620 Z= 0.373 Chirality : 0.050 0.128 180 Planarity : 0.004 0.028 208 Dihedral : 6.177 25.917 164 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -2.71 (0.56), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.011 0.002 PHE A 378 TYR 0.015 0.004 TYR B 310 ARG 0.006 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 18 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.131 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1515 time to fit residues: 2.8002 Evaluate side-chains 16 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.5112 r_free = 0.5112 target = 0.309026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.276614 restraints weight = 6055.514| |-----------------------------------------------------------------------------| r_work (start): 0.5076 rms_B_bonded: 6.73 r_work: 0.5139 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4924 r_free = 0.4924 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4924 r_free = 0.4924 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1210 Z= 0.153 Angle : 0.738 9.149 1620 Z= 0.342 Chirality : 0.048 0.126 180 Planarity : 0.003 0.030 208 Dihedral : 5.801 27.716 164 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.63 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.006 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 17 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.152 Fit side-chains REVERT: A 349 ARG cc_start: 0.5528 (mmp-170) cc_final: 0.4368 (ptm-80) outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1635 time to fit residues: 2.8660 Evaluate side-chains 16 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.5073 r_free = 0.5073 target = 0.303987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.267774 restraints weight = 9506.356| |-----------------------------------------------------------------------------| r_work (start): 0.5047 rms_B_bonded: 6.81 r_work: 0.5094 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4886 r_free = 0.4886 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4886 r_free = 0.4886 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1210 Z= 0.266 Angle : 0.805 9.170 1620 Z= 0.383 Chirality : 0.051 0.129 180 Planarity : 0.004 0.032 208 Dihedral : 6.157 26.322 164 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -2.85 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 330 PHE 0.011 0.002 PHE A 378 TYR 0.017 0.004 TYR A 310 ARG 0.005 0.001 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.03 seconds wall clock time: 23 minutes 8.19 seconds (1388.19 seconds total)