Starting phenix.real_space_refine on Mon Feb 10 19:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjm_4564/02_2025/6qjm_4564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjm_4564/02_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_4564/02_2025/6qjm_4564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjm_4564/02_2025/6qjm_4564.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjm_4564/02_2025/6qjm_4564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjm_4564/02_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-5592/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: 0.65, per 1000 atoms: 0.77 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: 0.19 Conformation dependent library (CDL) restraints added in 116.7 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: 0.11 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: 0.13 Time building geometry restraints manager: 0.23 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.050 ------------------------------------------------------------------------------- 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= 0.646 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 *********************** 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 : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1864 time to fit residues: 5.4046 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 : 0.117 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.158676 restraints weight = 1162.776| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 4.05 r_work: 0.4067 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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= 0.207 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 : 5.05 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 (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 (0.77), 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 *********************** 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 : 0.114 Fit side-chains REVERT: A 314 ASP cc_start: 0.7871 (m-30) cc_final: 0.7438 (p0) REVERT: B 314 ASP cc_start: 0.6027 (p0) cc_final: 0.5752 (p0) REVERT: C 285 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7551 (p) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1259 time to fit residues: 2.8550 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 : 0.115 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4395 r_free = 0.4395 target = 0.181571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.159292 restraints weight = 1128.453| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.70 r_work: 0.4138 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3703 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= 0.157 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 : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (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: -2.62 (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 *********************** 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 : 0.109 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1294 time to fit residues: 2.6174 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 : 0.098 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 overall best weight: 0.6003 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.183662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.161505 restraints weight = 1151.394| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.79 r_work: 0.4150 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4028 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= 0.144 Angle : 0.528 4.059 1125 Z= 0.272 Chirality : 0.053 0.125 144 Planarity : 0.003 0.015 132 Dihedral : 4.928 12.589 108 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.37 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: -2.36 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 310 *********************** 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 : 0.121 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1106 time to fit residues: 2.0769 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 : 0.114 ------------------------------------------------------------------------------- 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: 0.7980 chunk 6 optimal weight: 0.0470 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6353 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.184747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.161779 restraints weight = 1186.453| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.94 r_work: 0.4109 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 846 Z= 0.147 Angle : 0.528 3.993 1125 Z= 0.273 Chirality : 0.053 0.125 144 Planarity : 0.002 0.015 132 Dihedral : 4.751 12.424 108 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.81 % Allowed : 12.38 % 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: -2.30 (0.80), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 *********************** 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 18 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.119 Fit side-chains REVERT: A 314 ASP cc_start: 0.7901 (m-30) cc_final: 0.7542 (t0) REVERT: C 285 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7371 (p) REVERT: C 314 ASP cc_start: 0.6096 (p0) cc_final: 0.5355 (p0) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.1091 time to fit residues: 2.1677 Evaluate side-chains 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 285 SER 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: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.2233 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.177433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.156219 restraints weight = 1165.514| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.71 r_work: 0.4082 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4153 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= 0.204 Angle : 0.561 3.811 1125 Z= 0.290 Chirality : 0.054 0.133 144 Planarity : 0.002 0.013 132 Dihedral : 4.862 12.219 108 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 14.29 % 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: -2.45 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 310 *********************** 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 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.107 Fit side-chains REVERT: A 314 ASP cc_start: 0.8070 (m-30) cc_final: 0.7688 (t0) REVERT: B 283 ASP cc_start: 0.7956 (t0) cc_final: 0.7724 (t0) REVERT: C 314 ASP cc_start: 0.6219 (p0) cc_final: 0.5225 (p0) outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1066 time to fit residues: 1.8809 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 : 0.112 ------------------------------------------------------------------------------- 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=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: 0.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7985 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.183233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.161074 restraints weight = 1142.867| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.77 r_work: 0.4108 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 846 Z= 0.150 Angle : 0.545 4.327 1125 Z= 0.271 Chirality : 0.053 0.127 144 Planarity : 0.002 0.011 132 Dihedral : 4.717 12.245 108 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.86 % Allowed : 13.33 % 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: -2.36 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 *********************** 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: 3 poor density : 14 time to evaluate : 0.114 Fit side-chains REVERT: A 314 ASP cc_start: 0.8002 (m-30) cc_final: 0.7655 (t0) REVERT: C 314 ASP cc_start: 0.6250 (p0) cc_final: 0.5245 (p0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1144 time to fit residues: 2.1286 Evaluate side-chains 15 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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=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: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.7230 ------------------------------------------------------------------------------- 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 = 0.180304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.159248 restraints weight = 1144.150| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.64 r_work: 0.4117 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 846 Z= 0.153 Angle : 0.540 3.966 1125 Z= 0.273 Chirality : 0.053 0.126 144 Planarity : 0.002 0.011 132 Dihedral : 4.581 11.405 108 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.93 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: -2.30 (0.80), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 *********************** 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 16 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.117 Fit side-chains REVERT: A 314 ASP cc_start: 0.8093 (m-30) cc_final: 0.7668 (t0) REVERT: C 314 ASP cc_start: 0.6051 (p0) cc_final: 0.5051 (p0) outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1172 time to fit residues: 2.0588 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 : 0.132 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- 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: 0.0050 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.0040 overall best weight: 0.4763 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.182916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.161455 restraints weight = 1137.565| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.71 r_work: 0.4129 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 846 Z= 0.137 Angle : 0.528 3.933 1125 Z= 0.267 Chirality : 0.053 0.123 144 Planarity : 0.002 0.014 132 Dihedral : 4.452 11.543 108 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -2.20 (0.81), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.62), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 310 *********************** 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 : 0.116 Fit side-chains REVERT: A 314 ASP cc_start: 0.8003 (m-30) cc_final: 0.7599 (t0) REVERT: C 314 ASP cc_start: 0.6190 (p0) cc_final: 0.5175 (p0) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.1120 time to fit residues: 2.0887 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 : 0.113 ------------------------------------------------------------------------------- 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: 0.1980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9233 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.179222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.157961 restraints weight = 1196.595| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.76 r_work: 0.4113 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 846 Z= 0.176 Angle : 0.557 3.862 1125 Z= 0.283 Chirality : 0.052 0.130 144 Planarity : 0.002 0.013 132 Dihedral : 4.538 11.134 108 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 310 ********************** 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 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.109 Fit side-chains REVERT: A 314 ASP cc_start: 0.8048 (m-30) cc_final: 0.7641 (t0) REVERT: C 314 ASP cc_start: 0.6126 (p0) cc_final: 0.5119 (p0) outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.1259 time to fit residues: 1.8995 Evaluate side-chains 14 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.8238 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.179736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158772 restraints weight = 1161.017| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.66 r_work: 0.4120 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 846 Z= 0.156 Angle : 0.538 3.850 1125 Z= 0.271 Chirality : 0.053 0.127 144 Planarity : 0.002 0.011 132 Dihedral : 4.522 11.350 108 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 842.46 seconds wall clock time: 16 minutes 25.82 seconds (985.82 seconds total)