Starting phenix.real_space_refine on Wed Mar 5 15:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_13795.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_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/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_13795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_13795.map" model { file = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_13795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2025/7q3u_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-5624/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: 1.47, per 1000 atoms: 0.62 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: 0.55 Conformation dependent library (CDL) restraints added in 292.4 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: 0.23 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: 0.43 Time building geometry restraints manager: 0.64 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.780 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: 0.020 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.221 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: 0.1186 time to fit residues: 8.6052 Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.238823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.206258 restraints weight = 2512.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.211147 restraints weight = 1718.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.215055 restraints weight = 1249.754| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5821 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 to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.235 Fit side-chains REVERT: C 336 MET cc_start: 0.7703 (ptt) cc_final: 0.7220 (ptm) REVERT: D 286 GLN cc_start: 0.6490 (tt0) cc_final: 0.5769 (mt0) REVERT: D 323 MET cc_start: 0.7126 (ptm) cc_final: 0.5916 (ppp) REVERT: E 336 MET cc_start: 0.3203 (ptt) cc_final: 0.2518 (tpp) REVERT: E 345 ASN cc_start: 0.5489 (OUTLIER) cc_final: 0.5141 (m-40) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.1157 time to fit residues: 9.3316 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.253639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.222959 restraints weight = 2398.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.228239 restraints weight = 1530.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.232094 restraints weight = 1052.002| |-----------------------------------------------------------------------------| r_work (final): 0.5047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.6011 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= 0.233 Angle : 0.818 10.930 3175 Z= 0.435 Chirality : 0.042 0.142 275 Planarity : 0.005 0.050 465 Dihedral : 6.344 20.530 355 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % 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: -6.04 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 334 PHE 0.005 0.001 PHE E 283 ARG 0.002 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 60 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.234 Fit side-chains REVERT: A 331 GLN cc_start: 0.7353 (mm-40) cc_final: 0.6751 (mp10) REVERT: C 323 MET cc_start: 0.7513 (mtm) cc_final: 0.6049 (ttt) REVERT: C 336 MET cc_start: 0.7388 (ptt) cc_final: 0.6834 (ptp) REVERT: C 337 MET cc_start: 0.4581 (ptt) cc_final: 0.3968 (mtm) REVERT: D 323 MET cc_start: 0.6744 (ptm) cc_final: 0.5742 (ppp) REVERT: E 311 MET cc_start: 0.4167 (tmm) cc_final: 0.3693 (tpp) REVERT: E 319 ASN cc_start: 0.7140 (m-40) cc_final: 0.6246 (p0) REVERT: E 336 MET cc_start: 0.3007 (ptt) cc_final: 0.2573 (tpp) outliers start: 10 outliers final: 3 residues processed: 58 average time/residue: 0.0975 time to fit residues: 7.1460 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 MET 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 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** D 306 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** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.250120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.220322 restraints weight = 2390.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.225156 restraints weight = 1570.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.228813 restraints weight = 1113.981| |-----------------------------------------------------------------------------| r_work (final): 0.5050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.6759 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= 0.254 Angle : 0.793 11.169 3175 Z= 0.412 Chirality : 0.040 0.152 275 Planarity : 0.005 0.047 465 Dihedral : 6.382 21.702 355 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 4.76 % Allowed : 20.48 % 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: -6.12 (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 0.005 0.002 TRP D 334 PHE 0.007 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 60 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.245 Fit side-chains REVERT: A 331 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7289 (mp10) REVERT: C 323 MET cc_start: 0.7459 (mtm) cc_final: 0.6206 (ttt) REVERT: C 336 MET cc_start: 0.7466 (ptt) cc_final: 0.7130 (ptm) REVERT: C 337 MET cc_start: 0.5025 (ptt) cc_final: 0.4298 (mtm) REVERT: D 286 GLN cc_start: 0.6460 (tt0) cc_final: 0.5614 (mt0) REVERT: D 323 MET cc_start: 0.6714 (ptm) cc_final: 0.5768 (ppp) REVERT: E 289 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6202 (t80) REVERT: E 319 ASN cc_start: 0.7277 (m-40) cc_final: 0.6120 (p0) REVERT: E 336 MET cc_start: 0.3525 (ptt) cc_final: 0.2930 (tpp) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.1155 time to fit residues: 8.0416 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain D residue 318 ILE 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 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.233710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.205656 restraints weight = 2679.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.210111 restraints weight = 1745.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.213513 restraints weight = 1231.438| |-----------------------------------------------------------------------------| r_work (final): 0.4911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.7609 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= 0.325 Angle : 0.849 9.436 3175 Z= 0.449 Chirality : 0.046 0.271 275 Planarity : 0.005 0.052 465 Dihedral : 6.854 21.648 355 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 4.29 % Allowed : 23.33 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.13 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 334 PHE 0.010 0.002 PHE E 283 ARG 0.002 0.001 ARG E 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 59 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: C 323 MET cc_start: 0.7597 (mtm) cc_final: 0.6470 (ttt) REVERT: C 336 MET cc_start: 0.7394 (ptt) cc_final: 0.6870 (ptp) REVERT: D 289 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6161 (t80) REVERT: D 323 MET cc_start: 0.6997 (ptm) cc_final: 0.6229 (ppp) REVERT: E 336 MET cc_start: 0.3712 (ptt) cc_final: 0.2949 (tpp) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.0966 time to fit residues: 6.9531 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain D residue 289 PHE 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 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** E 327 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.242176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.212616 restraints weight = 2523.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.217105 restraints weight = 1657.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.220517 restraints weight = 1183.143| |-----------------------------------------------------------------------------| r_work (final): 0.4998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.7938 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= 0.214 Angle : 0.732 7.503 3175 Z= 0.382 Chirality : 0.055 0.381 275 Planarity : 0.004 0.046 465 Dihedral : 6.165 18.793 355 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.86 % Allowed : 24.76 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 334 PHE 0.006 0.001 PHE A 316 ARG 0.002 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 53 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.7431 (ttp) cc_final: 0.7165 (ttp) REVERT: A 343 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: B 307 MET cc_start: 0.7845 (ttt) cc_final: 0.7621 (ttt) REVERT: C 323 MET cc_start: 0.7369 (mtm) cc_final: 0.6255 (ttt) REVERT: C 336 MET cc_start: 0.7390 (ptt) cc_final: 0.7060 (ptp) REVERT: D 323 MET cc_start: 0.6973 (ptm) cc_final: 0.6189 (ppp) REVERT: E 285 ASN cc_start: 0.6099 (m110) cc_final: 0.5827 (m-40) REVERT: E 289 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6286 (t80) REVERT: E 336 MET cc_start: 0.3933 (ptt) cc_final: 0.3244 (tpp) outliers start: 6 outliers final: 0 residues processed: 52 average time/residue: 0.1109 time to fit residues: 7.2263 Evaluate side-chains 43 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN 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 32 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- 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 327 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.230189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.201432 restraints weight = 2538.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.205805 restraints weight = 1659.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.208933 restraints weight = 1182.915| |-----------------------------------------------------------------------------| r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.8659 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= 0.355 Angle : 0.860 8.548 3175 Z= 0.454 Chirality : 0.055 0.336 275 Planarity : 0.006 0.050 465 Dihedral : 7.194 23.839 355 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 2.86 % Allowed : 21.90 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.14 (0.21), 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 0.014 0.003 TRP D 334 PHE 0.010 0.002 PHE C 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 56 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: C 323 MET cc_start: 0.7193 (mtm) cc_final: 0.6381 (ttt) REVERT: C 336 MET cc_start: 0.7716 (ptt) cc_final: 0.7020 (ptp) REVERT: D 323 MET cc_start: 0.7430 (ptm) cc_final: 0.6423 (ppp) REVERT: E 336 MET cc_start: 0.5236 (ptt) cc_final: 0.4147 (tpp) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.0982 time to fit residues: 6.7082 Evaluate side-chains 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 303 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** 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 = 0.5154 r_free = 0.5154 target = 0.240991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.211652 restraints weight = 2503.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.216579 restraints weight = 1606.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.219961 restraints weight = 1128.322| |-----------------------------------------------------------------------------| r_work (final): 0.5043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.8810 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= 0.224 Angle : 0.753 7.859 3175 Z= 0.387 Chirality : 0.047 0.325 275 Planarity : 0.004 0.043 465 Dihedral : 6.254 20.974 355 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % 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: -6.05 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 334 PHE 0.006 0.001 PHE E 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 52 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.241 Fit side-chains REVERT: A 343 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: C 323 MET cc_start: 0.6889 (mtm) cc_final: 0.6169 (ttt) REVERT: C 336 MET cc_start: 0.7392 (ptt) cc_final: 0.6824 (ptp) REVERT: D 289 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.5705 (t80) REVERT: D 323 MET cc_start: 0.7251 (ptm) cc_final: 0.6405 (ppp) REVERT: E 322 MET cc_start: 0.6360 (mtt) cc_final: 0.6054 (mtt) REVERT: E 336 MET cc_start: 0.4501 (ptt) cc_final: 0.4125 (tpp) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.1037 time to fit residues: 6.7698 Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 10 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.250099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.218768 restraints weight = 2455.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.223177 restraints weight = 1670.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.226181 restraints weight = 1224.750| |-----------------------------------------------------------------------------| r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5821 moved from start: 0.8960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2390 Z= 0.208 Angle : 0.736 8.446 3175 Z= 0.378 Chirality : 0.050 0.359 275 Planarity : 0.004 0.043 465 Dihedral : 5.805 22.371 355 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.38 % Allowed : 24.76 % 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: -5.97 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 334 PHE 0.005 0.001 PHE C 313 ARG 0.003 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 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.236 Fit side-chains REVERT: A 307 MET cc_start: 0.7098 (ttp) cc_final: 0.6343 (tmm) REVERT: A 343 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: C 323 MET cc_start: 0.6859 (mtm) cc_final: 0.6048 (ttt) REVERT: C 330 LEU cc_start: 0.7754 (mp) cc_final: 0.7231 (tt) REVERT: C 336 MET cc_start: 0.7313 (ptt) cc_final: 0.6792 (ptp) REVERT: D 289 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5650 (t80) REVERT: D 323 MET cc_start: 0.7228 (ptm) cc_final: 0.6111 (ppp) REVERT: E 285 ASN cc_start: 0.6519 (m110) cc_final: 0.6260 (m-40) REVERT: E 322 MET cc_start: 0.5996 (mtt) cc_final: 0.5625 (mtt) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1045 time to fit residues: 6.3668 Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.0470 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 303 GLN ** 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 = 0.5145 r_free = 0.5145 target = 0.240539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.211171 restraints weight = 2557.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.215545 restraints weight = 1691.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.218716 restraints weight = 1215.818| |-----------------------------------------------------------------------------| r_work (final): 0.5049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2390 Z= 0.256 Angle : 0.757 7.372 3175 Z= 0.389 Chirality : 0.047 0.300 275 Planarity : 0.004 0.044 465 Dihedral : 6.105 24.611 355 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.38 % Allowed : 24.76 % 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: -5.96 (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 0.015 0.002 TRP C 334 PHE 0.006 0.001 PHE C 313 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 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.247 Fit side-chains REVERT: A 343 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: B 285 ASN cc_start: 0.7826 (m110) cc_final: 0.7615 (m110) REVERT: C 323 MET cc_start: 0.6940 (mtm) cc_final: 0.6322 (ttt) REVERT: C 336 MET cc_start: 0.7252 (ptt) cc_final: 0.6615 (ptp) REVERT: D 289 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5576 (t80) REVERT: D 323 MET cc_start: 0.7275 (ptm) cc_final: 0.6338 (ppp) REVERT: D 336 MET cc_start: 0.5822 (ptt) cc_final: 0.5579 (tpp) REVERT: E 322 MET cc_start: 0.5824 (mtt) cc_final: 0.5417 (mtt) REVERT: E 336 MET cc_start: 0.5297 (tpp) cc_final: 0.4835 (tpt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1057 time to fit residues: 6.5310 Evaluate side-chains 47 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 303 GLN ** 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 = 0.5283 r_free = 0.5283 target = 0.249309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.219646 restraints weight = 2401.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.223993 restraints weight = 1622.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.227103 restraints weight = 1181.750| |-----------------------------------------------------------------------------| r_work (final): 0.5183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.9482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2390 Z= 0.230 Angle : 0.725 8.230 3175 Z= 0.371 Chirality : 0.045 0.300 275 Planarity : 0.004 0.043 465 Dihedral : 5.909 23.742 355 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.38 % Allowed : 25.71 % 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: -5.92 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 PHE 0.006 0.001 PHE E 283 ARG 0.003 0.001 ARG D 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.47 seconds wall clock time: 24 minutes 22.91 seconds (1462.91 seconds total)