Starting phenix.real_space_refine on Sat Apr 26 14:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjm_4564/04_2025/6qjm_4564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjm_4564/04_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_4564/04_2025/6qjm_4564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjm_4564/04_2025/6qjm_4564.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjm_4564/04_2025/6qjm_4564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjm_4564/04_2025/6qjm_4564.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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B Time building chain proxies: 0.67, per 1000 atoms: 0.79 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: 0.52 Conformation dependent library (CDL) restraints added in 100.8 milliseconds 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: 0.13 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: 0.14 Time building geometry restraints manager: 0.56 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 'C' selection = chain 'B' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 7.360 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.510 ------------------------------------------------------------------------------- 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 (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: -2.36 (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 hydrogen bonds : bond 0.19059 ( 10) hydrogen bonds : angle 11.45780 ( 30) covalent geometry : bond 0.00979 ( 846) covalent geometry : angle 1.00602 ( 1125) *********************** 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 : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1396 time to fit residues: 4.0489 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 : 0.091 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.176745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153482 restraints weight = 1171.659| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 3.83 r_work: 0.4052 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 846 Z= 0.192 Angle : 0.724 5.934 1125 Z= 0.371 Chirality : 0.058 0.149 144 Planarity : 0.004 0.022 132 Dihedral : 6.092 14.451 108 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.95 % Allowed : 9.52 % 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 (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: -2.95 (0.74), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 10) hydrogen bonds : angle 8.26431 ( 30) covalent geometry : bond 0.00469 ( 846) covalent geometry : angle 0.72431 ( 1125) *********************** 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 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.100 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.1531 time to fit residues: 2.5762 Evaluate side-chains 12 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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** ** 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 = 0.4352 r_free = 0.4352 target = 0.183757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.160593 restraints weight = 1165.461| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.78 r_work: 0.4102 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 846 Z= 0.107 Angle : 0.561 4.133 1125 Z= 0.288 Chirality : 0.054 0.128 144 Planarity : 0.002 0.016 132 Dihedral : 5.449 14.024 108 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 10.48 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.74), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02526 ( 10) hydrogen bonds : angle 7.28600 ( 30) covalent geometry : bond 0.00254 ( 846) covalent geometry : angle 0.56085 ( 1125) *********************** 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 : 0.110 Fit side-chains REVERT: A 314 ASP cc_start: 0.7777 (m-30) cc_final: 0.7422 (m-30) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1565 time to fit residues: 3.1363 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 : 0.113 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.179715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158568 restraints weight = 1136.393| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.61 r_work: 0.4128 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3975 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= 0.101 Angle : 0.544 4.239 1125 Z= 0.282 Chirality : 0.053 0.125 144 Planarity : 0.002 0.013 132 Dihedral : 5.141 12.696 108 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.95 % Allowed : 15.24 % 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 (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: -2.65 (0.76), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02244 ( 10) hydrogen bonds : angle 6.87728 ( 30) covalent geometry : bond 0.00228 ( 846) covalent geometry : angle 0.54398 ( 1125) *********************** 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 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.145 Fit side-chains REVERT: B 284 LEU cc_start: 0.9262 (mp) cc_final: 0.9018 (mp) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.1170 time to fit residues: 2.0512 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 : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9233 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.177746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.156810 restraints weight = 1161.994| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.67 r_work: 0.4109 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 846 Z= 0.107 Angle : 0.537 3.958 1125 Z= 0.278 Chirality : 0.053 0.128 144 Planarity : 0.003 0.013 132 Dihedral : 5.024 12.761 108 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.95 % Allowed : 16.19 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.77), 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 0.003 0.001 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02233 ( 10) hydrogen bonds : angle 6.77156 ( 30) covalent geometry : bond 0.00251 ( 846) covalent geometry : angle 0.53672 ( 1125) *********************** 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 15 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.107 Fit side-chains REVERT: B 284 LEU cc_start: 0.9254 (mp) cc_final: 0.9027 (mp) outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.1140 time to fit residues: 1.8640 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 4 optimal weight: 0.0020 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9495 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.177062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156147 restraints weight = 1169.510| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.66 r_work: 0.4115 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4224 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= 0.113 Angle : 0.554 3.934 1125 Z= 0.287 Chirality : 0.054 0.128 144 Planarity : 0.002 0.012 132 Dihedral : 4.954 13.109 108 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (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: -2.50 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (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 hydrogen bonds : bond 0.02295 ( 10) hydrogen bonds : angle 6.62928 ( 30) covalent geometry : bond 0.00262 ( 846) covalent geometry : angle 0.55416 ( 1125) *********************** 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 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.113 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.1374 time to fit residues: 2.0728 Evaluate side-chains 13 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7230 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.182419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.159926 restraints weight = 1148.540| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.79 r_work: 0.4080 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 846 Z= 0.094 Angle : 0.545 4.696 1125 Z= 0.272 Chirality : 0.053 0.125 144 Planarity : 0.002 0.016 132 Dihedral : 4.724 12.102 108 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (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: -2.46 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02059 ( 10) hydrogen bonds : angle 6.21952 ( 30) covalent geometry : bond 0.00215 ( 846) covalent geometry : angle 0.54495 ( 1125) *********************** 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 17 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.111 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1103 time to fit residues: 2.0597 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 1.0733 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.176601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156246 restraints weight = 1160.703| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.55 r_work: 0.4086 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 846 Z= 0.123 Angle : 0.578 3.890 1125 Z= 0.297 Chirality : 0.054 0.132 144 Planarity : 0.002 0.014 132 Dihedral : 4.779 11.630 108 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 : 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 (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 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (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 hydrogen bonds : bond 0.02563 ( 10) hydrogen bonds : angle 6.59970 ( 30) covalent geometry : bond 0.00288 ( 846) covalent geometry : angle 0.57759 ( 1125) *********************** 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 15 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.105 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.1135 time to fit residues: 1.8459 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 : 0.097 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9735 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.177674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.156826 restraints weight = 1158.466| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.61 r_work: 0.4085 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 846 Z= 0.113 Angle : 0.563 3.909 1125 Z= 0.287 Chirality : 0.054 0.129 144 Planarity : 0.003 0.017 132 Dihedral : 4.742 12.562 108 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.49 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 (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: -2.54 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02354 ( 10) hydrogen bonds : angle 6.45425 ( 30) covalent geometry : bond 0.00260 ( 846) covalent geometry : angle 0.56266 ( 1125) *********************** 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 : 0.112 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1099 time to fit residues: 2.0505 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 : 0.111 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 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 = 0.4330 r_free = 0.4330 target = 0.177503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.156383 restraints weight = 1201.605| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.70 r_work: 0.4080 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 846 Z= 0.112 Angle : 0.571 4.032 1125 Z= 0.293 Chirality : 0.054 0.129 144 Planarity : 0.002 0.014 132 Dihedral : 4.697 11.810 108 Min Nonbonded Distance : 2.509 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 (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: -2.49 (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 0.002 0.000 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02280 ( 10) hydrogen bonds : angle 6.42464 ( 30) covalent geometry : bond 0.00256 ( 846) covalent geometry : angle 0.57127 ( 1125) ********************** 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 : 0.108 Fit side-chains REVERT: A 314 ASP cc_start: 0.8130 (m-30) cc_final: 0.7672 (t0) REVERT: B 283 ASP cc_start: 0.7681 (t0) cc_final: 0.7367 (t0) REVERT: C 314 ASP cc_start: 0.5891 (p0) cc_final: 0.5156 (p0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1169 time to fit residues: 2.1571 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 : 0.110 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.9483 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.177448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.156586 restraints weight = 1152.898| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.65 r_work: 0.4085 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 846 Z= 0.114 Angle : 0.570 3.989 1125 Z= 0.291 Chirality : 0.054 0.130 144 Planarity : 0.003 0.015 132 Dihedral : 4.690 11.894 108 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.49 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 (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: -2.54 (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 0.002 0.001 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 10) hydrogen bonds : angle 6.44200 ( 30) covalent geometry : bond 0.00263 ( 846) covalent geometry : angle 0.56979 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 899.48 seconds wall clock time: 16 minutes 48.50 seconds (1008.50 seconds total)