Starting phenix.real_space_refine on Thu Dec 7 16:14:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/12_2023/7q3u_13795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/12_2023/7q3u_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_13795/12_2023/7q3u_13795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/12_2023/7q3u_13795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/12_2023/7q3u_13795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/12_2023/7q3u_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-1.21rc1-5172/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: 1.57, per 1000 atoms: 0.67 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: 0.95 Conformation dependent library (CDL) restraints added in 500.7 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: 0.20 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: 0.47 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: 0.700 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: 3.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- 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 : 0.246 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1222 time to fit residues: 8.9815 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5394 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 2390 Z= 0.546 Angle : 1.140 7.951 3175 Z= 0.639 Chirality : 0.050 0.167 275 Planarity : 0.009 0.072 465 Dihedral : 8.473 25.296 355 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 34.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.42 % Favored : 80.58 % Rotamer: Outliers : 3.81 % Allowed : 21.43 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.06 (0.23), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.004 TRP C 334 PHE 0.020 0.004 PHE C 316 ARG 0.003 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 65 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.246 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.0963 time to fit residues: 7.9609 Evaluate side-chains 49 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0271 time to fit residues: 0.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** 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** ** 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** D 285 ASN D 344 GLN ** 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2390 Z= 0.226 Angle : 0.812 10.742 3175 Z= 0.428 Chirality : 0.042 0.159 275 Planarity : 0.005 0.055 465 Dihedral : 6.563 22.285 355 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 30.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.76 % Allowed : 21.43 % Favored : 73.81 % 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: -6.14 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 61 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.241 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 56 average time/residue: 0.1392 time to fit residues: 9.3726 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN D 344 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2390 Z= 0.339 Angle : 0.850 9.372 3175 Z= 0.450 Chirality : 0.045 0.206 275 Planarity : 0.006 0.058 465 Dihedral : 7.167 25.095 355 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 32.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.26 % Favored : 81.74 % Rotamer: Outliers : 3.81 % Allowed : 21.43 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.20 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 334 PHE 0.013 0.002 PHE C 289 ARG 0.003 0.001 ARG E 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 62 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.246 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 0.1156 time to fit residues: 8.5827 Evaluate side-chains 54 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0370 time to fit residues: 0.6126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.0040 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** 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: 0.5586 moved from start: 0.7914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2390 Z= 0.265 Angle : 0.778 8.495 3175 Z= 0.409 Chirality : 0.053 0.385 275 Planarity : 0.006 0.058 465 Dihedral : 6.562 23.465 355 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 2.86 % Allowed : 23.81 % 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: -6.18 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 334 PHE 0.008 0.002 PHE C 289 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 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.231 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.1065 time to fit residues: 7.1612 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0448 time to fit residues: 0.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 18 optimal weight: 0.0060 chunk 33 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.1332 ------------------------------------------------------------------------------- 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 306 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2390 Z= 0.157 Angle : 0.637 7.121 3175 Z= 0.333 Chirality : 0.045 0.356 275 Planarity : 0.004 0.047 465 Dihedral : 5.435 17.339 355 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.95 % Allowed : 25.24 % Favored : 73.81 % 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: -6.00 (0.19), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 PHE 0.004 0.001 PHE C 313 ARG 0.003 0.001 ARG B 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 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.237 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.1052 time to fit residues: 6.5600 Evaluate side-chains 43 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** 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: 0.5584 moved from start: 0.8473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2390 Z= 0.249 Angle : 0.703 6.254 3175 Z= 0.370 Chirality : 0.044 0.343 275 Planarity : 0.005 0.048 465 Dihedral : 5.981 20.713 355 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 1.90 % Allowed : 22.86 % 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: -5.97 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 334 PHE 0.007 0.002 PHE A 289 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 53 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.240 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.1000 time to fit residues: 6.7172 Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0268 time to fit residues: 0.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 0.0770 chunk 18 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.8682 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= 0.206 Angle : 0.676 7.661 3175 Z= 0.351 Chirality : 0.044 0.336 275 Planarity : 0.005 0.049 465 Dihedral : 5.814 19.637 355 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.48 % Allowed : 25.71 % Favored : 73.81 % 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: -6.02 (0.19), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 PHE 0.005 0.001 PHE A 289 ARG 0.002 0.001 ARG B 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 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.245 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1064 time to fit residues: 6.2411 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0305 time to fit residues: 0.3410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 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 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** 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: 0.5568 moved from start: 0.8944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2390 Z= 0.244 Angle : 0.697 6.824 3175 Z= 0.362 Chirality : 0.044 0.304 275 Planarity : 0.005 0.049 465 Dihedral : 5.930 19.379 355 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.94 % Favored : 84.06 % Rotamer: Outliers : 0.00 % Allowed : 27.14 % 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: -6.01 (0.19), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 334 PHE 0.009 0.001 PHE E 283 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 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1174 time to fit residues: 6.6446 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** ** C 343 GLN ** 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: 0.5533 moved from start: 0.9172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2390 Z= 0.220 Angle : 0.679 6.846 3175 Z= 0.353 Chirality : 0.044 0.294 275 Planarity : 0.005 0.050 465 Dihedral : 5.905 19.683 355 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 26.19 % Favored : 73.81 % 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: -6.01 (0.19), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.010 0.001 PHE E 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 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.254 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1140 time to fit residues: 6.6331 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** 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 = 0.5077 r_free = 0.5077 target = 0.237012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.208684 restraints weight = 2547.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.213020 restraints weight = 1689.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.216172 restraints weight = 1211.207| |-----------------------------------------------------------------------------| r_work (final): 0.4998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.9470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2390 Z= 0.247 Angle : 0.737 6.606 3175 Z= 0.382 Chirality : 0.045 0.286 275 Planarity : 0.005 0.052 465 Dihedral : 6.071 21.442 355 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 0.00 % Allowed : 26.19 % Favored : 73.81 % 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: -6.03 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 PHE 0.008 0.002 PHE A 289 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: 1120.05 seconds wall clock time: 20 minutes 59.34 seconds (1259.34 seconds total)