Starting phenix.real_space_refine on Sun Mar 10 14:48:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/03_2024/7q3u_13795.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 1400 2.51 5 N 450 2.21 5 O 470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2355 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 471 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 471 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 471 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 471 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 471 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Time building chain proxies: 1.65, per 1000 atoms: 0.70 Number of scatterers: 2355 At special positions: 0 Unit cell: (55.12, 68.9, 41.34, 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 35 16.00 O 470 8.00 N 450 7.00 C 1400 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 - 3.50 Amino acid : False - 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: 0.96 Conformation dependent library (CDL) restraints added in 444.6 milliseconds 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.565A pdb=" N SER A 317 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER B 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER D 317 " --> pdb=" O ILE E 318 " (cutoff:3.500A) 8 hydrogen bonds defined for protein. 21 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: 0.45 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 775 1.33 - 1.45: 396 1.45 - 1.57: 1149 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 2390 Sorted by residual: bond pdb=" CG GLN A 343 " pdb=" CD GLN A 343 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CG GLN E 343 " pdb=" CD GLN E 343 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CG GLN C 343 " pdb=" CD GLN C 343 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" CG GLN D 343 " pdb=" CD GLN D 343 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" CG GLN B 343 " pdb=" CD GLN B 343 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.56e+00 ... (remaining 2385 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.89: 90 106.89 - 113.63: 1060 113.63 - 120.38: 828 120.38 - 127.12: 1177 127.12 - 133.86: 20 Bond angle restraints: 3175 Sorted by residual: angle pdb=" N MET C 307 " pdb=" CA MET C 307 " pdb=" C MET C 307 " ideal model delta sigma weight residual 111.30 106.42 4.88 1.43e+00 4.89e-01 1.16e+01 angle pdb=" N MET A 307 " pdb=" CA MET A 307 " pdb=" C MET A 307 " ideal model delta sigma weight residual 111.30 106.44 4.86 1.43e+00 4.89e-01 1.16e+01 angle pdb=" N MET E 307 " pdb=" CA MET E 307 " pdb=" C MET E 307 " ideal model delta sigma weight residual 111.30 106.45 4.85 1.43e+00 4.89e-01 1.15e+01 angle pdb=" N MET D 307 " pdb=" CA MET D 307 " pdb=" C MET D 307 " ideal model delta sigma weight residual 111.30 106.47 4.83 1.43e+00 4.89e-01 1.14e+01 angle pdb=" N MET B 307 " pdb=" CA MET B 307 " pdb=" C MET B 307 " ideal model delta sigma weight residual 111.30 106.48 4.82 1.43e+00 4.89e-01 1.14e+01 ... (remaining 3170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1165 17.75 - 35.50: 145 35.50 - 53.25: 10 53.25 - 71.00: 5 71.00 - 88.75: 10 Dihedral angle restraints: 1335 sinusoidal: 475 harmonic: 860 Sorted by residual: dihedral pdb=" CA MET C 337 " pdb=" C MET C 337 " pdb=" N GLY C 338 " pdb=" CA GLY C 338 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET B 337 " pdb=" C MET B 337 " pdb=" N GLY B 338 " pdb=" CA GLY B 338 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET D 337 " pdb=" C MET D 337 " pdb=" N GLY D 338 " pdb=" CA GLY D 338 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 1332 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.036: 158 0.036 - 0.072: 80 0.072 - 0.108: 32 0.108 - 0.144: 0 0.144 - 0.180: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CB ILE B 318 " pdb=" CA ILE B 318 " pdb=" CG1 ILE B 318 " pdb=" CG2 ILE B 318 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CB ILE A 318 " pdb=" CA ILE A 318 " pdb=" CG1 ILE A 318 " pdb=" CG2 ILE A 318 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CB ILE E 318 " pdb=" CA ILE E 318 " pdb=" CG1 ILE E 318 " pdb=" CG2 ILE E 318 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.94e-01 ... (remaining 272 not shown) Planarity restraints: 465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 348 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 349 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 348 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO B 349 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 348 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO E 349 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 349 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 349 " -0.025 5.00e-02 4.00e+02 ... (remaining 462 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 93 2.68 - 3.23: 2401 3.23 - 3.79: 3973 3.79 - 4.34: 5200 4.34 - 4.90: 9748 Nonbonded interactions: 21415 Sorted by model distance: nonbonded pdb=" NE2 GLN A 331 " pdb=" OG SER D 347 " model vdw 2.120 2.520 nonbonded pdb=" OG SER B 347 " pdb=" NE2 GLN C 331 " model vdw 2.165 2.520 nonbonded pdb=" OD1 ASN B 301 " pdb=" N ASN B 302 " model vdw 2.355 2.520 nonbonded pdb=" OD1 ASN E 301 " pdb=" N ASN E 302 " model vdw 2.355 2.520 nonbonded pdb=" OD1 ASN D 301 " pdb=" N ASN D 302 " model vdw 2.355 2.520 ... (remaining 21410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.850 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: 3.350 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.570 Find NCS groups from input model: 0.180 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4561 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 : 0.005 0.041 2390 Z= 0.347 Angle : 1.167 9.569 3175 Z= 0.647 Chirality : 0.049 0.180 275 Planarity : 0.006 0.046 465 Dihedral : 16.840 88.755 825 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 36.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % 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: -5.79 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 334 PHE 0.004 0.001 PHE E 316 ARG 0.004 0.002 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 306 ASN cc_start: 0.7211 (m110) cc_final: 0.6821 (m110) REVERT: C 311 MET cc_start: 0.5155 (mtp) cc_final: 0.4872 (mtt) REVERT: C 323 MET cc_start: 0.6237 (ptm) cc_final: 0.5684 (mtm) REVERT: E 336 MET cc_start: 0.4106 (ptt) cc_final: 0.3128 (tpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1042 time to fit residues: 7.5441 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 2390 Z= 0.585 Angle : 1.190 8.315 3175 Z= 0.666 Chirality : 0.052 0.177 275 Planarity : 0.009 0.070 465 Dihedral : 8.765 23.207 355 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 34.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.45 % Favored : 78.55 % Rotamer: Outliers : 4.29 % Allowed : 20.48 % Favored : 75.24 % 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: -6.07 (0.23), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.18), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.004 TRP C 334 PHE 0.019 0.004 PHE C 316 ARG 0.004 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.6911 (ptt) cc_final: 0.6407 (ptm) REVERT: D 285 ASN cc_start: 0.6624 (m-40) cc_final: 0.6265 (m-40) REVERT: D 323 MET cc_start: 0.7109 (ptm) cc_final: 0.5387 (ppp) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.0962 time to fit residues: 8.0774 Evaluate side-chains 54 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 0.0170 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN C 285 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2390 Z= 0.192 Angle : 0.779 11.220 3175 Z= 0.409 Chirality : 0.044 0.268 275 Planarity : 0.005 0.051 465 Dihedral : 6.310 18.903 355 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 5.71 % Allowed : 21.43 % Favored : 72.86 % 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: -6.10 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.65 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 334 PHE 0.007 0.001 PHE A 316 ARG 0.003 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.232 Fit side-chains REVERT: C 336 MET cc_start: 0.6883 (ptt) cc_final: 0.6327 (ptm) REVERT: C 337 MET cc_start: 0.4688 (ptt) cc_final: 0.3851 (mtm) REVERT: D 323 MET cc_start: 0.6479 (ptm) cc_final: 0.4958 (ppp) outliers start: 12 outliers final: 1 residues processed: 60 average time/residue: 0.1331 time to fit residues: 9.5333 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.0070 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2390 Z= 0.255 Angle : 0.758 8.705 3175 Z= 0.402 Chirality : 0.045 0.270 275 Planarity : 0.005 0.053 465 Dihedral : 6.451 25.561 355 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 3.33 % Allowed : 24.29 % Favored : 72.38 % 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: -6.08 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 334 PHE 0.006 0.002 PHE C 316 ARG 0.002 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.264 Fit side-chains REVERT: A 307 MET cc_start: 0.7036 (ttp) cc_final: 0.6148 (tmm) REVERT: A 323 MET cc_start: 0.6851 (mtm) cc_final: 0.5369 (ttt) REVERT: C 336 MET cc_start: 0.6942 (ptt) cc_final: 0.6476 (ptm) REVERT: D 323 MET cc_start: 0.6635 (ptm) cc_final: 0.5255 (ppp) REVERT: E 336 MET cc_start: 0.2695 (ptt) cc_final: 0.2217 (ttt) outliers start: 7 outliers final: 2 residues processed: 51 average time/residue: 0.1181 time to fit residues: 7.4579 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 303 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.0060 chunk 2 optimal weight: 0.0670 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2390 Z= 0.240 Angle : 0.748 7.781 3175 Z= 0.393 Chirality : 0.051 0.349 275 Planarity : 0.005 0.053 465 Dihedral : 6.304 22.032 355 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 1.90 % Allowed : 26.67 % Favored : 71.43 % 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: -6.09 (0.19), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 334 PHE 0.007 0.001 PHE B 283 ARG 0.002 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.243 Fit side-chains REVERT: A 323 MET cc_start: 0.7037 (mtm) cc_final: 0.5424 (ttt) REVERT: B 307 MET cc_start: 0.7550 (ttt) cc_final: 0.7280 (ttt) REVERT: C 336 MET cc_start: 0.7039 (ptt) cc_final: 0.6650 (ptm) REVERT: D 323 MET cc_start: 0.6790 (ptm) cc_final: 0.5373 (ppp) REVERT: E 336 MET cc_start: 0.3219 (ptt) cc_final: 0.2473 (ttt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.1169 time to fit residues: 7.2060 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN C 285 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2390 Z= 0.258 Angle : 0.744 7.077 3175 Z= 0.391 Chirality : 0.047 0.343 275 Planarity : 0.005 0.053 465 Dihedral : 6.332 18.475 355 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 4.29 % Allowed : 24.76 % Favored : 70.95 % 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: -6.08 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 334 PHE 0.007 0.002 PHE B 283 ARG 0.002 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7064 (mtm) cc_final: 0.5280 (ttt) REVERT: C 323 MET cc_start: 0.7530 (mtm) cc_final: 0.5659 (ttt) REVERT: C 336 MET cc_start: 0.6993 (ptt) cc_final: 0.6539 (ptm) REVERT: D 323 MET cc_start: 0.6782 (ptm) cc_final: 0.5426 (ppp) REVERT: E 311 MET cc_start: 0.4718 (tmm) cc_final: 0.4397 (tpp) REVERT: E 336 MET cc_start: 0.3816 (ptt) cc_final: 0.3052 (tpp) outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.1042 time to fit residues: 6.7264 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.8675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2390 Z= 0.319 Angle : 0.798 7.412 3175 Z= 0.424 Chirality : 0.051 0.325 275 Planarity : 0.006 0.059 465 Dihedral : 6.797 21.091 355 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 35.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 3.81 % Allowed : 26.19 % Favored : 70.00 % 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: -6.17 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 334 PHE 0.008 0.002 PHE E 283 ARG 0.002 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.6984 (mtm) cc_final: 0.5198 (ttt) REVERT: C 307 MET cc_start: 0.6876 (ttp) cc_final: 0.6339 (ttp) REVERT: C 323 MET cc_start: 0.7581 (mtm) cc_final: 0.5858 (ttt) REVERT: C 336 MET cc_start: 0.7152 (ptt) cc_final: 0.6816 (ptm) REVERT: D 323 MET cc_start: 0.6909 (ptm) cc_final: 0.5511 (ppp) REVERT: D 336 MET cc_start: 0.6509 (ptt) cc_final: 0.5985 (ptt) REVERT: E 336 MET cc_start: 0.4386 (ptt) cc_final: 0.3730 (tpp) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.1019 time to fit residues: 6.7688 Evaluate side-chains 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.0570 chunk 29 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN C 285 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.8826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2390 Z= 0.182 Angle : 0.663 5.626 3175 Z= 0.349 Chirality : 0.050 0.334 275 Planarity : 0.005 0.051 465 Dihedral : 5.634 16.310 355 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.38 % Allowed : 27.62 % Favored : 70.00 % 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: -6.08 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 334 PHE 0.008 0.001 PHE E 283 ARG 0.003 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7006 (mtm) cc_final: 0.5191 (ttt) REVERT: C 323 MET cc_start: 0.7388 (mtm) cc_final: 0.5647 (ttt) REVERT: C 336 MET cc_start: 0.6975 (ptt) cc_final: 0.6772 (ptm) REVERT: D 323 MET cc_start: 0.6649 (ptm) cc_final: 0.5086 (ppp) REVERT: E 336 MET cc_start: 0.4016 (ptt) cc_final: 0.3571 (tpp) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.0998 time to fit residues: 6.7890 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN C 285 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5615 moved from start: 0.9079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2390 Z= 0.279 Angle : 0.744 7.885 3175 Z= 0.389 Chirality : 0.049 0.311 275 Planarity : 0.005 0.052 465 Dihedral : 6.140 17.425 355 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 1.43 % Allowed : 25.24 % Favored : 73.33 % 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: -6.12 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 PHE 0.007 0.001 PHE E 313 ARG 0.002 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7065 (mtm) cc_final: 0.5274 (ttt) REVERT: C 323 MET cc_start: 0.7455 (mtm) cc_final: 0.5923 (ttt) REVERT: C 336 MET cc_start: 0.7432 (ptt) cc_final: 0.6702 (ptp) REVERT: D 323 MET cc_start: 0.6773 (ptm) cc_final: 0.5319 (ppp) REVERT: D 336 MET cc_start: 0.6215 (ptt) cc_final: 0.5816 (ptt) REVERT: E 336 MET cc_start: 0.4668 (ptt) cc_final: 0.4373 (tpp) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.1030 time to fit residues: 6.5523 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.9280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2390 Z= 0.267 Angle : 0.719 5.931 3175 Z= 0.378 Chirality : 0.048 0.305 275 Planarity : 0.005 0.054 465 Dihedral : 6.202 19.259 355 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 28.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.38 % Allowed : 25.24 % Favored : 72.38 % 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: -6.09 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 PHE 0.012 0.002 PHE A 283 ARG 0.002 0.001 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.7810 (mtm) cc_final: 0.7554 (mtm) REVERT: A 323 MET cc_start: 0.6908 (mtm) cc_final: 0.5338 (ttt) REVERT: C 323 MET cc_start: 0.7494 (mtm) cc_final: 0.5938 (ttt) REVERT: C 336 MET cc_start: 0.7324 (ptt) cc_final: 0.6734 (ptp) REVERT: D 323 MET cc_start: 0.7090 (ptm) cc_final: 0.5521 (ppp) REVERT: D 336 MET cc_start: 0.6304 (ptt) cc_final: 0.6097 (ptt) REVERT: E 336 MET cc_start: 0.4765 (ptt) cc_final: 0.4366 (tpt) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1063 time to fit residues: 6.6949 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain E residue 322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 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 = 0.5087 r_free = 0.5087 target = 0.231290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.202783 restraints weight = 2574.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.207066 restraints weight = 1702.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.210269 restraints weight = 1223.749| |-----------------------------------------------------------------------------| r_work (final): 0.4984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.9597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2390 Z= 0.289 Angle : 0.751 7.048 3175 Z= 0.393 Chirality : 0.048 0.309 275 Planarity : 0.006 0.056 465 Dihedral : 6.345 18.997 355 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 2.86 % Allowed : 25.24 % Favored : 71.90 % 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: -6.09 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 334 PHE 0.009 0.002 PHE E 283 ARG 0.002 0.001 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.72 seconds wall clock time: 21 minutes 49.46 seconds (1309.46 seconds total)