Starting phenix.real_space_refine on Wed Sep 17 02:59:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjm_4564/09_2025/6qjm_4564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjm_4564/09_2025/6qjm_4564.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/6qjm_4564/09_2025/6qjm_4564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjm_4564/09_2025/6qjm_4564.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjm_4564/09_2025/6qjm_4564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjm_4564/09_2025/6qjm_4564.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.014 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 3 5.16 5 C 537 2.51 5 N 147 2.21 5 O 159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 846 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.21, per 1000 atoms: 0.25 Number of scatterers: 846 At special positions: 0 Unit cell: (59.34, 57.96, 38.64, 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 3 16.00 O 159 8.00 N 147 7.00 C 537 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: 0.04 Conformation dependent library (CDL) restraints added in 20.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 210 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 275 through 280 removed outlier: 6.853A pdb=" N VAL A 275 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 277 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS B 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN A 279 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 283 through 288 removed outlier: 6.903A pdb=" N LEU A 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASP A 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N ASN C 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER A 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN C 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.095A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.116A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 5.893A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 hydrogen bond angles 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: 0.09 Time building geometry restraints manager: 0.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 219 1.33 - 1.45: 101 1.45 - 1.57: 523 1.57 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 846 Sorted by residual: bond pdb=" CA SER C 285 " pdb=" CB SER C 285 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.24e-02 6.50e+03 2.36e+00 bond pdb=" CA SER B 285 " pdb=" CB SER B 285 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.24e-02 6.50e+03 2.23e+00 bond pdb=" CA SER A 285 " pdb=" CB SER A 285 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.24e-02 6.50e+03 2.17e+00 bond pdb=" CG ASN B 279 " pdb=" ND2 ASN B 279 " ideal model delta sigma weight residual 1.328 1.303 0.025 2.10e-02 2.27e+03 1.46e+00 bond pdb=" CA SER C 316 " pdb=" CB SER C 316 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.72e-02 3.38e+03 1.46e+00 ... (remaining 841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 959 1.15 - 2.29: 129 2.29 - 3.44: 19 3.44 - 4.58: 12 4.58 - 5.73: 6 Bond angle restraints: 1125 Sorted by residual: angle pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta sigma weight residual 121.80 126.66 -4.86 2.44e+00 1.68e-01 3.98e+00 angle pdb=" C TYR B 310 " pdb=" N LYS B 311 " pdb=" CA LYS B 311 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" C TYR C 310 " pdb=" N LYS C 311 " pdb=" CA LYS C 311 " ideal model delta sigma weight residual 121.80 126.64 -4.84 2.44e+00 1.68e-01 3.94e+00 angle pdb=" C LYS C 281 " pdb=" N LEU C 282 " pdb=" CA LEU C 282 " ideal model delta sigma weight residual 122.07 118.85 3.22 1.71e+00 3.42e-01 3.54e+00 angle pdb=" C LYS B 281 " pdb=" N LEU B 282 " pdb=" CA LEU B 282 " ideal model delta sigma weight residual 122.07 118.86 3.21 1.71e+00 3.42e-01 3.52e+00 ... (remaining 1120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.03: 382 5.03 - 10.07: 107 10.07 - 15.10: 33 15.10 - 20.13: 9 20.13 - 25.16: 12 Dihedral angle restraints: 543 sinusoidal: 225 harmonic: 318 Sorted by residual: dihedral pdb=" CA SER B 316 " pdb=" C SER B 316 " pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER A 316 " pdb=" C SER A 316 " pdb=" N LYS A 317 " pdb=" CA LYS A 317 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N LYS C 317 " pdb=" CA LYS C 317 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 540 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.038: 40 0.038 - 0.072: 51 0.072 - 0.105: 29 0.105 - 0.139: 21 0.139 - 0.172: 3 Chirality restraints: 144 Sorted by residual: chirality pdb=" CG LEU A 284 " pdb=" CB LEU A 284 " pdb=" CD1 LEU A 284 " pdb=" CD2 LEU A 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CG LEU C 284 " pdb=" CB LEU C 284 " pdb=" CD1 LEU C 284 " pdb=" CD2 LEU C 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CG LEU B 284 " pdb=" CB LEU B 284 " pdb=" CD1 LEU B 284 " pdb=" CD2 LEU B 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 141 not shown) Planarity restraints: 132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 279 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" CG ASN A 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 279 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" CG ASN C 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 279 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASN B 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 129 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 310 2.91 - 3.40: 693 3.40 - 3.90: 1259 3.90 - 4.40: 1147 4.40 - 4.90: 2511 Nonbonded interactions: 5920 Sorted by model distance: nonbonded pdb=" OG SER A 285 " pdb=" O SER B 285 " model vdw 2.408 3.040 nonbonded pdb=" O SER A 285 " pdb=" OG SER C 285 " model vdw 2.408 3.040 nonbonded pdb=" O LYS A 321 " pdb=" O SER C 320 " model vdw 2.516 3.040 nonbonded pdb=" OG SER A 285 " pdb=" N ASN A 286 " model vdw 2.521 3.120 nonbonded pdb=" OG SER B 285 " pdb=" N ASN B 286 " model vdw 2.521 3.120 ... (remaining 5915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.120 Find NCS groups from input model: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.010 0.031 846 Z= 0.487 Angle : 1.006 5.731 1125 Z= 0.519 Chirality : 0.073 0.172 144 Planarity : 0.006 0.024 132 Dihedral : 8.063 25.161 333 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.83), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.005 TYR A 310 Details of bonding type rmsd covalent geometry : bond 0.00979 ( 846) covalent geometry : angle 1.00602 ( 1125) hydrogen bonds : bond 0.19059 ( 10) hydrogen bonds : angle 11.45780 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0784 time to fit residues: 2.2606 Evaluate side-chains 11 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9745 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 279 ASN C 276 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158673 restraints weight = 1155.908| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 4.05 r_work: 0.4068 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 846 Z= 0.132 Angle : 0.653 6.182 1125 Z= 0.334 Chirality : 0.056 0.136 144 Planarity : 0.004 0.021 132 Dihedral : 5.830 14.647 108 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.95 % Allowed : 6.67 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 846) covalent geometry : angle 0.65266 ( 1125) hydrogen bonds : bond 0.02906 ( 10) hydrogen bonds : angle 7.90749 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.037 Fit side-chains REVERT: A 314 ASP cc_start: 0.7871 (m-30) cc_final: 0.7437 (p0) REVERT: B 314 ASP cc_start: 0.6028 (p0) cc_final: 0.5754 (p0) REVERT: C 285 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7549 (p) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0582 time to fit residues: 1.3254 Evaluate side-chains 15 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.181544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.159144 restraints weight = 1144.626| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.73 r_work: 0.4136 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 846 Z= 0.102 Angle : 0.547 4.149 1125 Z= 0.283 Chirality : 0.053 0.125 144 Planarity : 0.003 0.014 132 Dihedral : 5.302 13.374 108 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 8.57 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 846) covalent geometry : angle 0.54665 ( 1125) hydrogen bonds : bond 0.02446 ( 10) hydrogen bonds : angle 7.20103 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.040 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0614 time to fit residues: 1.2350 Evaluate side-chains 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9483 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** 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 = 0.4356 r_free = 0.4356 target = 0.178674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.157551 restraints weight = 1127.666| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.64 r_work: 0.4101 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 846 Z= 0.115 Angle : 0.557 3.954 1125 Z= 0.288 Chirality : 0.053 0.127 144 Planarity : 0.003 0.015 132 Dihedral : 5.083 12.852 108 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.90 % Allowed : 9.52 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 846) covalent geometry : angle 0.55696 ( 1125) hydrogen bonds : bond 0.02243 ( 10) hydrogen bonds : angle 6.94040 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.039 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0503 time to fit residues: 0.9261 Evaluate side-chains 15 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.8730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** 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 = 0.4368 r_free = 0.4368 target = 0.181718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.159168 restraints weight = 1211.172| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.87 r_work: 0.4089 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 846 Z= 0.107 Angle : 0.559 4.158 1125 Z= 0.285 Chirality : 0.053 0.128 144 Planarity : 0.002 0.012 132 Dihedral : 4.961 12.676 108 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.86 % Allowed : 12.38 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 846) covalent geometry : angle 0.55941 ( 1125) hydrogen bonds : bond 0.02181 ( 10) hydrogen bonds : angle 6.62864 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.040 Fit side-chains REVERT: A 314 ASP cc_start: 0.8073 (m-30) cc_final: 0.7662 (t0) REVERT: C 314 ASP cc_start: 0.6241 (p0) cc_final: 0.5327 (p0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.0501 time to fit residues: 0.9256 Evaluate side-chains 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 1.4233 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.175416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.154900 restraints weight = 1153.590| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.59 r_work: 0.4088 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 846 Z= 0.149 Angle : 0.590 3.837 1125 Z= 0.304 Chirality : 0.054 0.136 144 Planarity : 0.002 0.011 132 Dihedral : 5.044 13.156 108 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.75), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 846) covalent geometry : angle 0.59015 ( 1125) hydrogen bonds : bond 0.02717 ( 10) hydrogen bonds : angle 6.88018 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.041 Fit side-chains REVERT: A 314 ASP cc_start: 0.8068 (m-30) cc_final: 0.7430 (p0) REVERT: B 314 ASP cc_start: 0.5265 (p0) cc_final: 0.5002 (p0) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0497 time to fit residues: 0.9187 Evaluate side-chains 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.2238 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.176457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156148 restraints weight = 1162.578| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.51 r_work: 0.4090 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 846 Z= 0.132 Angle : 0.590 3.947 1125 Z= 0.303 Chirality : 0.054 0.133 144 Planarity : 0.003 0.015 132 Dihedral : 4.977 13.393 108 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.90 % Allowed : 18.10 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.76), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 310 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 846) covalent geometry : angle 0.58967 ( 1125) hydrogen bonds : bond 0.02522 ( 10) hydrogen bonds : angle 6.74301 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.040 Fit side-chains REVERT: A 314 ASP cc_start: 0.8079 (m-30) cc_final: 0.7460 (p0) REVERT: B 314 ASP cc_start: 0.5221 (p0) cc_final: 0.4948 (p0) outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.0576 time to fit residues: 0.8602 Evaluate side-chains 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 8 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.181878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.160492 restraints weight = 1180.936| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.71 r_work: 0.4117 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 846 Z= 0.091 Angle : 0.540 4.062 1125 Z= 0.275 Chirality : 0.053 0.124 144 Planarity : 0.002 0.012 132 Dihedral : 4.676 12.143 108 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 17.14 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.80), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 846) covalent geometry : angle 0.54030 ( 1125) hydrogen bonds : bond 0.01894 ( 10) hydrogen bonds : angle 6.21757 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.041 Fit side-chains REVERT: A 314 ASP cc_start: 0.8029 (m-30) cc_final: 0.7680 (t0) REVERT: B 283 ASP cc_start: 0.7473 (t0) cc_final: 0.7193 (t0) REVERT: C 314 ASP cc_start: 0.5889 (p0) cc_final: 0.5181 (p0) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0488 time to fit residues: 0.9036 Evaluate side-chains 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.157458 restraints weight = 1176.454| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.69 r_work: 0.4098 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 846 Z= 0.110 Angle : 0.554 3.946 1125 Z= 0.283 Chirality : 0.053 0.130 144 Planarity : 0.002 0.010 132 Dihedral : 4.661 11.773 108 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 16.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 846) covalent geometry : angle 0.55417 ( 1125) hydrogen bonds : bond 0.02310 ( 10) hydrogen bonds : angle 6.40611 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.041 Fit side-chains REVERT: A 314 ASP cc_start: 0.8142 (m-30) cc_final: 0.7443 (p0) REVERT: B 283 ASP cc_start: 0.7621 (t0) cc_final: 0.7314 (t0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.0501 time to fit residues: 0.9258 Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1235 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.176800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155946 restraints weight = 1138.925| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.62 r_work: 0.4078 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 846 Z= 0.128 Angle : 0.584 4.066 1125 Z= 0.302 Chirality : 0.054 0.134 144 Planarity : 0.003 0.017 132 Dihedral : 4.757 12.767 108 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 310 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 846) covalent geometry : angle 0.58436 ( 1125) hydrogen bonds : bond 0.02388 ( 10) hydrogen bonds : angle 6.59440 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.041 Fit side-chains REVERT: A 314 ASP cc_start: 0.8169 (m-30) cc_final: 0.7713 (t0) REVERT: B 283 ASP cc_start: 0.7731 (t0) cc_final: 0.7394 (t0) REVERT: C 314 ASP cc_start: 0.6002 (p0) cc_final: 0.5346 (p0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.0544 time to fit residues: 0.9957 Evaluate side-chains 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8485 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.178339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.156934 restraints weight = 1186.729| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.73 r_work: 0.4090 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 846 Z= 0.106 Angle : 0.558 3.989 1125 Z= 0.285 Chirality : 0.053 0.128 144 Planarity : 0.003 0.016 132 Dihedral : 4.663 12.315 108 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.86 % Allowed : 16.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 310 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 846) covalent geometry : angle 0.55796 ( 1125) hydrogen bonds : bond 0.02209 ( 10) hydrogen bonds : angle 6.39223 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 489.92 seconds wall clock time: 9 minutes 55.28 seconds (595.28 seconds total)