Starting phenix.real_space_refine on Mon Feb 10 20:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3u_13795/02_2025/7q3u_13795.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3u_13795/02_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_13795/02_2025/7q3u_13795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3u_13795/02_2025/7q3u_13795.map" model { file = "/net/cci-nas-00/data/ceres_data/7q3u_13795/02_2025/7q3u_13795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3u_13795/02_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-5592/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: 1.50, per 1000 atoms: 0.64 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: 0.60 Conformation dependent library (CDL) restraints added in 327.5 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: 0.17 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: 0.42 Time building geometry restraints manager: 0.69 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: 0.800 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- 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 : 0.212 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: 0.1043 time to fit residues: 7.5068 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 : 0.266 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.206154 restraints weight = 2512.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.211050 restraints weight = 1718.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.214976 restraints weight = 1254.219| |-----------------------------------------------------------------------------| r_work (final): 0.4891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 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 : 0.233 Fit side-chains REVERT: C 336 MET cc_start: 0.7699 (ptt) cc_final: 0.7214 (ptm) REVERT: D 286 GLN cc_start: 0.6487 (tt0) cc_final: 0.5765 (mt0) REVERT: D 323 MET cc_start: 0.7126 (ptm) cc_final: 0.5907 (ppp) REVERT: E 336 MET cc_start: 0.3200 (ptt) cc_final: 0.2512 (tpp) REVERT: E 345 ASN cc_start: 0.5492 (OUTLIER) cc_final: 0.5140 (m-40) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.1101 time to fit residues: 8.8445 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 : 0.236 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.253419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.222538 restraints weight = 2393.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.227593 restraints weight = 1529.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.231468 restraints weight = 1062.409| |-----------------------------------------------------------------------------| r_work (final): 0.5042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2390 Z= 0.244 Angle : 0.817 10.662 3175 Z= 0.434 Chirality : 0.042 0.136 275 Planarity : 0.005 0.048 465 Dihedral : 6.368 20.736 355 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.76 % Allowed : 21.90 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.05 (0.20), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.15), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 334 PHE 0.006 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 61 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.213 Fit side-chains REVERT: A 331 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6753 (mp10) REVERT: C 323 MET cc_start: 0.7530 (mtm) cc_final: 0.6051 (ttt) REVERT: C 336 MET cc_start: 0.7397 (ptt) cc_final: 0.7083 (ptm) REVERT: C 337 MET cc_start: 0.4515 (ptt) cc_final: 0.3922 (mtm) REVERT: D 323 MET cc_start: 0.6735 (ptm) cc_final: 0.5737 (ppp) REVERT: E 311 MET cc_start: 0.4385 (tmm) cc_final: 0.3575 (tpp) REVERT: E 319 ASN cc_start: 0.7172 (m-40) cc_final: 0.6268 (p0) REVERT: E 336 MET cc_start: 0.2963 (ptt) cc_final: 0.2449 (tpp) outliers start: 10 outliers final: 3 residues processed: 59 average time/residue: 0.0987 time to fit residues: 7.3732 Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.239534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.209679 restraints weight = 2434.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.214781 restraints weight = 1573.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.218454 restraints weight = 1102.314| |-----------------------------------------------------------------------------| r_work (final): 0.4972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2390 Z= 0.323 Angle : 0.861 11.091 3175 Z= 0.453 Chirality : 0.042 0.155 275 Planarity : 0.006 0.049 465 Dihedral : 6.987 24.390 355 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % 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: -6.12 (0.20), 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 0.005 0.002 TRP C 334 PHE 0.010 0.002 PHE E 283 ARG 0.001 0.000 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: 9 poor density : 51 time to evaluate : 0.217 Fit side-chains REVERT: C 323 MET cc_start: 0.7629 (mtm) cc_final: 0.6412 (ttt) REVERT: C 337 MET cc_start: 0.5416 (ptt) cc_final: 0.4419 (mtm) REVERT: D 286 GLN cc_start: 0.6532 (tt0) cc_final: 0.5655 (mt0) REVERT: D 307 MET cc_start: 0.7338 (ttt) cc_final: 0.7123 (ttt) REVERT: D 323 MET cc_start: 0.7072 (ptm) cc_final: 0.6167 (ppp) REVERT: E 289 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6581 (t80) REVERT: E 319 ASN cc_start: 0.7339 (m-40) cc_final: 0.6057 (p0) REVERT: E 336 MET cc_start: 0.3565 (ptt) cc_final: 0.2759 (tpp) outliers start: 9 outliers final: 2 residues processed: 57 average time/residue: 0.1178 time to fit residues: 8.2169 Evaluate side-chains 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 MET 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: 0.5980 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 306 ASN E 327 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.245128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.214509 restraints weight = 2440.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.219039 restraints weight = 1628.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.222819 restraints weight = 1180.279| |-----------------------------------------------------------------------------| r_work (final): 0.5053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2390 Z= 0.233 Angle : 0.758 7.504 3175 Z= 0.399 Chirality : 0.047 0.320 275 Planarity : 0.005 0.046 465 Dihedral : 6.270 19.393 355 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.76 % Allowed : 25.71 % Favored : 69.52 % 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 0.008 0.002 TRP C 334 PHE 0.007 0.001 PHE E 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 60 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: C 323 MET cc_start: 0.7402 (mtm) cc_final: 0.6298 (ttt) REVERT: D 323 MET cc_start: 0.6889 (ptm) cc_final: 0.6015 (ppp) REVERT: E 289 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6533 (t80) REVERT: E 336 MET cc_start: 0.3608 (ptt) cc_final: 0.2949 (tpp) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.0996 time to fit residues: 7.3151 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** 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 = 0.5031 r_free = 0.5031 target = 0.228992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.202082 restraints weight = 2589.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.205898 restraints weight = 1731.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.208749 restraints weight = 1254.303| |-----------------------------------------------------------------------------| r_work (final): 0.4911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.8338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2390 Z= 0.327 Angle : 0.844 8.523 3175 Z= 0.444 Chirality : 0.047 0.276 275 Planarity : 0.005 0.050 465 Dihedral : 6.913 22.392 355 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.97 % Favored : 82.03 % Rotamer: Outliers : 4.76 % Allowed : 21.90 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.07 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 334 PHE 0.010 0.002 PHE E 283 ARG 0.002 0.001 ARG E 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 59 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASN cc_start: 0.7953 (m110) cc_final: 0.7748 (m110) REVERT: C 323 MET cc_start: 0.7326 (mtm) cc_final: 0.6313 (ttt) REVERT: D 289 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6112 (t80) REVERT: D 323 MET cc_start: 0.7438 (ptm) cc_final: 0.6449 (ppp) REVERT: E 336 MET cc_start: 0.4689 (ptt) cc_final: 0.3699 (tpp) REVERT: E 337 MET cc_start: 0.5572 (mtm) cc_final: 0.5349 (mtm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.1002 time to fit residues: 7.0839 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 322 MET Chi-restraints excluded: chain D 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: 0.8980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 346 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.219755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.193085 restraints weight = 2721.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.196938 restraints weight = 1753.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.199677 restraints weight = 1243.920| |-----------------------------------------------------------------------------| r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.9302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 2390 Z= 0.454 Angle : 0.959 8.588 3175 Z= 0.508 Chirality : 0.056 0.321 275 Planarity : 0.006 0.051 465 Dihedral : 7.802 25.329 355 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.42 % Favored : 80.58 % Rotamer: Outliers : 5.24 % Allowed : 23.33 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.17 (0.22), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 334 PHE 0.014 0.003 PHE E 283 ARG 0.002 0.001 ARG D 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 62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASN cc_start: 0.8383 (m110) cc_final: 0.8093 (m110) REVERT: C 323 MET cc_start: 0.7107 (mtm) cc_final: 0.6357 (ttt) REVERT: D 289 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6137 (t80) REVERT: D 323 MET cc_start: 0.7598 (ptm) cc_final: 0.6558 (ppp) REVERT: E 316 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6820 (t80) REVERT: E 336 MET cc_start: 0.5949 (ptt) cc_final: 0.4767 (tpp) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.1044 time to fit residues: 7.3290 Evaluate side-chains 57 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 322 MET Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain E residue 316 PHE 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: 2.9990 chunk 19 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 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 = 0.5252 r_free = 0.5252 target = 0.249553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.219355 restraints weight = 2532.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.223369 restraints weight = 1655.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.226345 restraints weight = 1192.593| |-----------------------------------------------------------------------------| r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.9428 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= 0.258 Angle : 0.771 7.345 3175 Z= 0.404 Chirality : 0.050 0.295 275 Planarity : 0.004 0.044 465 Dihedral : 6.664 21.013 355 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer: Outliers : 3.81 % Allowed : 23.81 % 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: -6.11 (0.21), 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 0.012 0.002 TRP C 334 PHE 0.007 0.001 PHE E 283 ARG 0.003 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 54 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 SER cc_start: 0.6591 (t) cc_final: 0.6377 (m) REVERT: B 307 MET cc_start: 0.7689 (ttt) cc_final: 0.7042 (ttt) REVERT: C 323 MET cc_start: 0.6789 (mtm) cc_final: 0.6186 (ttt) REVERT: D 289 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.5802 (t80) REVERT: D 323 MET cc_start: 0.7437 (ptm) cc_final: 0.6527 (ppp) REVERT: E 336 MET cc_start: 0.4815 (ptt) cc_final: 0.4361 (tpp) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1285 time to fit residues: 8.3865 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 : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 322 MET 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: 0.6980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 10 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 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 = 0.248143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.219911 restraints weight = 2420.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.223909 restraints weight = 1628.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.226846 restraints weight = 1183.295| |-----------------------------------------------------------------------------| r_work (final): 0.5112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.9543 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= 0.207 Angle : 0.724 6.554 3175 Z= 0.377 Chirality : 0.047 0.253 275 Planarity : 0.004 0.041 465 Dihedral : 6.232 20.067 355 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 3.33 % Allowed : 25.24 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.03 (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 0.013 0.002 TRP C 334 PHE 0.009 0.001 PHE A 283 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 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: B 285 ASN cc_start: 0.8017 (m110) cc_final: 0.7780 (m110) REVERT: B 307 MET cc_start: 0.7572 (ttt) cc_final: 0.7010 (ttt) REVERT: C 323 MET cc_start: 0.6702 (mtm) cc_final: 0.6137 (ttt) REVERT: D 289 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5574 (t80) REVERT: D 323 MET cc_start: 0.7409 (ptm) cc_final: 0.6391 (ppp) REVERT: E 336 MET cc_start: 0.5156 (ptt) cc_final: 0.4876 (tpp) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.1034 time to fit residues: 6.8822 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN 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 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: 0.0370 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** 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 = 0.5225 r_free = 0.5225 target = 0.247427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.217664 restraints weight = 2426.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.221860 restraints weight = 1615.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.225039 restraints weight = 1168.186| |-----------------------------------------------------------------------------| r_work (final): 0.5115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.9692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2390 Z= 0.221 Angle : 0.724 5.878 3175 Z= 0.379 Chirality : 0.046 0.271 275 Planarity : 0.004 0.038 465 Dihedral : 6.208 19.703 355 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 3.81 % Allowed : 25.24 % 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: -6.02 (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 0.002 TRP C 334 PHE 0.010 0.001 PHE A 283 ARG 0.003 0.001 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: B 307 MET cc_start: 0.7585 (ttt) cc_final: 0.7092 (ttt) REVERT: C 323 MET cc_start: 0.6689 (mtm) cc_final: 0.6095 (ttt) REVERT: D 289 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5585 (t80) REVERT: D 323 MET cc_start: 0.7250 (ptm) cc_final: 0.6192 (ppp) REVERT: D 339 MET cc_start: 0.4929 (ptm) cc_final: 0.4447 (ptm) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.1057 time to fit residues: 7.0274 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 302 ASN 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: 0.6980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 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 285 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** 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 = 0.5243 r_free = 0.5243 target = 0.245462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.216794 restraints weight = 2431.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.220633 restraints weight = 1661.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.223455 restraints weight = 1220.080| |-----------------------------------------------------------------------------| r_work (final): 0.5133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.9964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 2390 Z= 0.286 Angle : 0.750 5.883 3175 Z= 0.399 Chirality : 0.056 0.415 275 Planarity : 0.004 0.050 465 Dihedral : 6.372 19.868 355 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 3.33 % Allowed : 25.71 % 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: -6.07 (0.19), 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 0.014 0.002 TRP C 334 PHE 0.011 0.001 PHE A 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: 1288.29 seconds wall clock time: 23 minutes 57.60 seconds (1437.60 seconds total)