Starting phenix.real_space_refine on Mon Sep 23 12:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/09_2024/7q3u_13795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/09_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_13795/09_2024/7q3u_13795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/09_2024/7q3u_13795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/09_2024/7q3u_13795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3u_13795/09_2024/7q3u_13795.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2355 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D Time building chain proxies: 1.67, per 1000 atoms: 0.71 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 314.4 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: 0.22 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: 0.44 Time building geometry restraints manager: 0.70 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: 0.00 - 1.91: 2940 1.91 - 3.83: 155 3.83 - 5.74: 70 5.74 - 7.66: 5 7.66 - 9.57: 5 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 3.120 nonbonded pdb=" OG SER B 347 " pdb=" NE2 GLN C 331 " model vdw 2.165 3.120 nonbonded pdb=" OD1 ASN B 301 " pdb=" N ASN B 302 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASN E 301 " pdb=" N ASN E 302 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASN D 301 " pdb=" N ASN D 302 " model vdw 2.355 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- 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 : 0.226 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: 0.1020 time to fit residues: 7.3773 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 7.9990 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: 4.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 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** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 2390 Z= 0.458 Angle : 1.042 7.687 3175 Z= 0.580 Chirality : 0.048 0.140 275 Planarity : 0.008 0.064 465 Dihedral : 7.736 23.073 355 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 2.86 % Allowed : 19.52 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.23), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 334 PHE 0.015 0.003 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 67 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.233 Fit side-chains REVERT: C 336 MET cc_start: 0.7446 (ptt) cc_final: 0.6873 (ptm) REVERT: D 286 GLN cc_start: 0.6584 (tt0) cc_final: 0.5759 (mt0) REVERT: D 323 MET cc_start: 0.6863 (ptm) cc_final: 0.5161 (ppp) REVERT: E 336 MET cc_start: 0.3298 (ptt) cc_final: 0.2239 (tpp) REVERT: E 345 ASN cc_start: 0.5535 (OUTLIER) cc_final: 0.5119 (m-40) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.1123 time to fit residues: 9.0426 Evaluate side-chains 48 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 345 ASN 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: 0.5980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 285 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN C 285 ASN C 306 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 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: 0.5330 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2390 Z= 0.221 Angle : 0.803 11.083 3175 Z= 0.425 Chirality : 0.041 0.136 275 Planarity : 0.005 0.047 465 Dihedral : 6.206 19.901 355 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.29 % Allowed : 21.90 % 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 0.011 0.002 TRP D 334 PHE 0.005 0.001 PHE E 283 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 59 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.255 Fit side-chains REVERT: A 331 GLN cc_start: 0.6680 (mm-40) cc_final: 0.6265 (mp10) REVERT: C 323 MET cc_start: 0.7627 (mtm) cc_final: 0.5774 (ttt) REVERT: C 337 MET cc_start: 0.4306 (ptt) cc_final: 0.3715 (mtm) REVERT: D 323 MET cc_start: 0.6395 (ptm) cc_final: 0.4799 (ppp) REVERT: E 311 MET cc_start: 0.4187 (tmm) cc_final: 0.3780 (tpp) REVERT: E 319 ASN cc_start: 0.7364 (m-40) cc_final: 0.6467 (p0) REVERT: E 336 MET cc_start: 0.2710 (ptt) cc_final: 0.2157 (tpp) outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 0.0946 time to fit residues: 6.9504 Evaluate side-chains 48 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** C 285 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN E 306 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2390 Z= 0.304 Angle : 0.825 9.393 3175 Z= 0.440 Chirality : 0.042 0.152 275 Planarity : 0.006 0.047 465 Dihedral : 6.649 22.787 355 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 4.29 % Allowed : 20.00 % Favored : 75.71 % 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: -6.11 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.65 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 334 PHE 0.008 0.002 PHE E 283 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 58 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.222 Fit side-chains REVERT: C 323 MET cc_start: 0.7614 (mtm) cc_final: 0.6015 (ttt) REVERT: C 336 MET cc_start: 0.6944 (ptt) cc_final: 0.6645 (ptm) REVERT: C 337 MET cc_start: 0.4361 (ptt) cc_final: 0.3474 (mtm) REVERT: D 323 MET cc_start: 0.6771 (ptm) cc_final: 0.5382 (ppp) REVERT: E 289 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6297 (t80) REVERT: E 319 ASN cc_start: 0.7433 (m-40) cc_final: 0.6081 (p0) REVERT: E 336 MET cc_start: 0.3522 (ptt) cc_final: 0.2653 (tpp) outliers start: 9 outliers final: 1 residues processed: 55 average time/residue: 0.1184 time to fit residues: 7.9278 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 289 PHE 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: 0.8980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN C 285 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2390 Z= 0.279 Angle : 0.792 7.620 3175 Z= 0.421 Chirality : 0.045 0.239 275 Planarity : 0.005 0.049 465 Dihedral : 6.432 19.791 355 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 6.67 % Allowed : 22.38 % 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: -6.12 (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 0.007 0.002 TRP C 334 PHE 0.008 0.002 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 64 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.7407 (ttt) cc_final: 0.7148 (ttt) REVERT: C 323 MET cc_start: 0.7554 (mtm) cc_final: 0.6147 (ttt) REVERT: C 331 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: C 336 MET cc_start: 0.6861 (ptt) cc_final: 0.6419 (ptp) REVERT: D 323 MET cc_start: 0.6661 (ptm) cc_final: 0.5215 (ppp) REVERT: E 285 ASN cc_start: 0.5986 (m110) cc_final: 0.5745 (m-40) REVERT: E 336 MET cc_start: 0.3760 (ptt) cc_final: 0.2995 (tpp) outliers start: 14 outliers final: 4 residues processed: 58 average time/residue: 0.0976 time to fit residues: 7.1509 Evaluate side-chains 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain D residue 345 ASN 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: 2.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2390 Z= 0.235 Angle : 0.730 6.163 3175 Z= 0.380 Chirality : 0.050 0.315 275 Planarity : 0.004 0.045 465 Dihedral : 5.901 18.321 355 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.29 % Allowed : 23.81 % 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: -6.07 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 334 PHE 0.006 0.001 PHE B 283 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 58 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.7048 (ttp) cc_final: 0.6515 (tmm) REVERT: A 343 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: B 285 ASN cc_start: 0.7910 (m110) cc_final: 0.7609 (m110) REVERT: C 323 MET cc_start: 0.7395 (mtm) cc_final: 0.5976 (ttt) REVERT: C 330 LEU cc_start: 0.7077 (mp) cc_final: 0.6535 (tt) REVERT: D 289 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5363 (t80) REVERT: D 323 MET cc_start: 0.6481 (ptm) cc_final: 0.5249 (ppp) REVERT: E 285 ASN cc_start: 0.6033 (m110) cc_final: 0.5815 (m-40) REVERT: E 289 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6113 (t80) REVERT: E 311 MET cc_start: 0.4429 (tmm) cc_final: 0.4084 (tpp) REVERT: E 336 MET cc_start: 0.3695 (ptt) cc_final: 0.2889 (tpp) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 0.0995 time to fit residues: 7.0226 Evaluate side-chains 49 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 289 PHE 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: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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: 0.5553 moved from start: 0.8462 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= 0.268 Angle : 0.742 6.832 3175 Z= 0.390 Chirality : 0.044 0.231 275 Planarity : 0.005 0.043 465 Dihedral : 6.190 19.307 355 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 3.33 % Allowed : 22.86 % 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 0.007 0.002 PHE B 283 ARG 0.001 0.000 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 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: B 318 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6801 (pt) REVERT: C 323 MET cc_start: 0.7475 (mtm) cc_final: 0.6089 (ttt) REVERT: D 289 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5256 (t80) REVERT: D 323 MET cc_start: 0.6727 (ptm) cc_final: 0.5371 (ppp) REVERT: D 336 MET cc_start: 0.6310 (ptt) cc_final: 0.5763 (ptt) REVERT: E 311 MET cc_start: 0.4807 (tmm) cc_final: 0.4599 (tpp) REVERT: E 336 MET cc_start: 0.4286 (ptt) cc_final: 0.3603 (tpp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.0990 time to fit residues: 6.6128 Evaluate side-chains 52 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 345 ASN 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: 0.8980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** B 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: 0.5537 moved from start: 0.8741 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= 0.249 Angle : 0.738 7.522 3175 Z= 0.385 Chirality : 0.043 0.223 275 Planarity : 0.004 0.041 465 Dihedral : 6.091 20.777 355 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 2.38 % Allowed : 23.81 % 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: -6.04 (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 0.011 0.002 TRP C 334 PHE 0.007 0.001 PHE B 283 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 49 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.229 Fit side-chains REVERT: A 307 MET cc_start: 0.7145 (ttp) cc_final: 0.6347 (tmm) REVERT: A 343 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: C 323 MET cc_start: 0.7407 (mtm) cc_final: 0.6004 (ttt) REVERT: D 289 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5273 (t80) REVERT: D 323 MET cc_start: 0.6690 (ptm) cc_final: 0.5416 (ppp) REVERT: D 336 MET cc_start: 0.6514 (ptt) cc_final: 0.6136 (ptt) REVERT: E 336 MET cc_start: 0.4247 (ptt) cc_final: 0.3351 (tpp) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.0995 time to fit residues: 6.0515 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain D residue 289 PHE 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: 2.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.5548 moved from start: 0.9009 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= 0.238 Angle : 0.743 8.940 3175 Z= 0.389 Chirality : 0.042 0.215 275 Planarity : 0.004 0.046 465 Dihedral : 5.967 19.893 355 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 2.86 % Allowed : 24.29 % 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 (0.20), 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 0.013 0.001 TRP C 334 PHE 0.007 0.001 PHE B 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 52 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.232 Fit side-chains REVERT: A 307 MET cc_start: 0.7185 (ttp) cc_final: 0.6387 (tmm) REVERT: A 343 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: C 323 MET cc_start: 0.7333 (mtm) cc_final: 0.5997 (ttt) REVERT: D 289 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5201 (t80) REVERT: D 323 MET cc_start: 0.6820 (ptm) cc_final: 0.5449 (ppp) REVERT: D 336 MET cc_start: 0.6579 (ptt) cc_final: 0.6098 (ptt) REVERT: E 336 MET cc_start: 0.4378 (ptt) cc_final: 0.3507 (tpt) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.0998 time to fit residues: 6.3852 Evaluate side-chains 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain D residue 289 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 346 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN C 285 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** 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: 0.5638 moved from start: 0.9413 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= 0.298 Angle : 0.792 9.481 3175 Z= 0.419 Chirality : 0.047 0.352 275 Planarity : 0.005 0.052 465 Dihedral : 6.351 21.007 355 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 2.38 % Allowed : 23.81 % 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: -6.08 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 PHE 0.008 0.002 PHE D 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 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.231 Fit side-chains REVERT: A 343 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: C 323 MET cc_start: 0.7245 (mtm) cc_final: 0.6057 (ttt) REVERT: D 289 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5201 (t80) REVERT: D 323 MET cc_start: 0.7073 (ptm) cc_final: 0.5556 (ppp) REVERT: D 336 MET cc_start: 0.6617 (ptt) cc_final: 0.6343 (ptt) REVERT: E 336 MET cc_start: 0.5138 (ptt) cc_final: 0.4140 (tpp) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.0974 time to fit residues: 6.5094 Evaluate side-chains 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain D residue 289 PHE 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: 3.9990 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 1 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.243065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.216267 restraints weight = 2451.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.220169 restraints weight = 1622.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.223120 restraints weight = 1168.366| |-----------------------------------------------------------------------------| r_work (final): 0.5072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.9627 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= 0.192 Angle : 0.699 8.824 3175 Z= 0.365 Chirality : 0.045 0.286 275 Planarity : 0.004 0.054 465 Dihedral : 5.686 16.814 355 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.38 % Allowed : 26.19 % 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: -5.99 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.006 0.001 PHE B 283 ARG 0.003 0.001 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1101.47 seconds wall clock time: 20 minutes 19.98 seconds (1219.98 seconds total)