Starting phenix.real_space_refine on Tue Mar 19 16:58:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/03_2024/8jma_36411_neut_trim_updated.pdb" } resolution = 2.5 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= 0.006 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7848 2.51 5 N 2056 2.21 5 O 2120 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.42, per 1000 atoms: 0.42 Number of scatterers: 24568 At special positions: 0 Unit cell: (110.67, 110.67, 105.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2120 8.00 N 2056 7.00 C 7848 6.00 H 12472 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 79.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 38 through 63 Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.550A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 160 Processing helix chain 'A' and resid 169 through 214 removed outlier: 3.905A pdb=" N TYR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 263 through 320 removed outlier: 6.068A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 356 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.945A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 424 removed outlier: 3.727A pdb=" N ILE A 420 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 421 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 38 through 63 Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.550A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 160 Processing helix chain 'B' and resid 169 through 214 removed outlier: 3.905A pdb=" N TYR B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 263 through 320 removed outlier: 6.068A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 356 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.945A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 424 removed outlier: 3.706A pdb=" N ILE B 420 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 421 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 38 through 63 Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.550A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 160 Processing helix chain 'C' and resid 169 through 214 removed outlier: 3.905A pdb=" N TYR C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix Processing helix chain 'C' and resid 263 through 320 removed outlier: 6.068A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 356 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 372 through 387 removed outlier: 3.945A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 424 removed outlier: 3.721A pdb=" N ILE C 420 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 421 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 38 through 63 Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.550A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 125 through 160 Processing helix chain 'D' and resid 169 through 214 removed outlier: 3.905A pdb=" N TYR D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 263 through 320 removed outlier: 6.068A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 356 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 372 through 387 removed outlier: 3.945A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 424 removed outlier: 3.722A pdb=" N ILE D 420 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 421 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 26 Processing sheet with id= B, first strand: chain 'B' and resid 22 through 26 Processing sheet with id= C, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= D, first strand: chain 'D' and resid 22 through 26 992 hydrogen bonds defined for protein. 2760 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: 9.27 Time building geometry restraints manager: 22.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12440 1.02 - 1.21: 32 1.21 - 1.41: 5022 1.41 - 1.61: 7194 1.61 - 1.81: 112 Bond restraints: 24800 Sorted by residual: bond pdb=" C2 FRU C 501 " pdb=" O5 FRU C 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 FRU B 501 " pdb=" O5 FRU B 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 FRU D 501 " pdb=" O5 FRU D 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C2 FRU A 501 " pdb=" O5 FRU A 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 FRU B 501 " pdb=" O5 FRU B 501 " ideal model delta sigma weight residual 1.420 1.486 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 24795 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.11: 413 107.11 - 113.89: 29588 113.89 - 120.67: 9077 120.67 - 127.46: 5606 127.46 - 134.24: 108 Bond angle restraints: 44792 Sorted by residual: angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 112.02 107.82 4.20 1.31e+00 5.83e-01 1.03e+01 angle pdb=" C ILE D 418 " pdb=" CA ILE D 418 " pdb=" CB ILE D 418 " ideal model delta sigma weight residual 112.02 107.85 4.17 1.31e+00 5.83e-01 1.01e+01 angle pdb=" C ILE C 418 " pdb=" CA ILE C 418 " pdb=" CB ILE C 418 " ideal model delta sigma weight residual 112.02 107.87 4.15 1.31e+00 5.83e-01 1.00e+01 angle pdb=" C ILE B 418 " pdb=" CA ILE B 418 " pdb=" CB ILE B 418 " ideal model delta sigma weight residual 112.02 107.91 4.11 1.31e+00 5.83e-01 9.86e+00 angle pdb=" C VAL A 417 " pdb=" CA VAL A 417 " pdb=" CB VAL A 417 " ideal model delta sigma weight residual 112.14 108.36 3.78 1.35e+00 5.49e-01 7.85e+00 ... (remaining 44787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 10306 17.25 - 34.50: 910 34.50 - 51.75: 220 51.75 - 69.00: 160 69.00 - 86.25: 8 Dihedral angle restraints: 11604 sinusoidal: 6272 harmonic: 5332 Sorted by residual: dihedral pdb=" CB GLU B 66 " pdb=" CG GLU B 66 " pdb=" CD GLU B 66 " pdb=" OE1 GLU B 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.25 -86.25 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " pdb=" CD GLU A 66 " pdb=" OE1 GLU A 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU D 66 " pdb=" CG GLU D 66 " pdb=" CD GLU D 66 " pdb=" OE1 GLU D 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 11601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1212 0.025 - 0.050: 474 0.050 - 0.075: 252 0.075 - 0.100: 50 0.100 - 0.125: 24 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 3 " pdb=" N ILE B 3 " pdb=" C ILE B 3 " pdb=" CB ILE B 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE D 3 " pdb=" N ILE D 3 " pdb=" C ILE D 3 " pdb=" CB ILE D 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 2009 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 413 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA A 413 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 413 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 414 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 413 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA D 413 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA D 413 " 0.015 2.00e-02 2.50e+03 pdb=" N THR D 414 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 413 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA B 413 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 413 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 414 " -0.013 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1775 2.21 - 2.80: 52371 2.80 - 3.40: 73665 3.40 - 4.00: 94635 4.00 - 4.60: 147507 Nonbonded interactions: 369953 Sorted by model distance: nonbonded pdb=" OD1 ASN A 401 " pdb=" HG1 THR A 403 " model vdw 1.607 1.850 nonbonded pdb=" OD1 ASN D 401 " pdb=" HG1 THR D 403 " model vdw 1.608 1.850 nonbonded pdb=" OD1 ASN B 401 " pdb=" HG1 THR B 403 " model vdw 1.608 1.850 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.608 1.850 nonbonded pdb=" H ASN C 27 " pdb=" O ARG C 31 " model vdw 1.615 1.850 ... (remaining 369948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.610 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: 0.350 Extract box with map and model: 4.540 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 79.720 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.004 0.071 12328 Z= 0.287 Angle : 0.512 5.813 16728 Z= 0.282 Chirality : 0.035 0.125 2012 Planarity : 0.004 0.022 2040 Dihedral : 16.386 86.254 4472 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 17.93 % Favored : 81.46 % 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: 3.05 (0.21), residues: 1508 helix: 2.43 (0.14), residues: 1264 sheet: 1.30 (0.74), residues: 48 loop : -0.65 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE A 298 TYR 0.007 0.001 TYR A 415 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.543 Fit side-chains REVERT: A 33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7336 (mp0) REVERT: B 33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7335 (mp0) REVERT: C 33 GLU cc_start: 0.7562 (mp0) cc_final: 0.7333 (mp0) REVERT: D 33 GLU cc_start: 0.7559 (mp0) cc_final: 0.7334 (mp0) outliers start: 8 outliers final: 8 residues processed: 168 average time/residue: 2.5465 time to fit residues: 467.9023 Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12328 Z= 0.239 Angle : 0.443 4.170 16728 Z= 0.248 Chirality : 0.035 0.124 2012 Planarity : 0.004 0.022 2040 Dihedral : 3.969 23.505 1764 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.52 % Allowed : 16.41 % Favored : 82.07 % 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: 2.93 (0.21), residues: 1508 helix: 2.34 (0.14), residues: 1264 sheet: 1.36 (0.75), residues: 48 loop : -0.70 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE A 298 TYR 0.011 0.001 TYR D 415 ARG 0.002 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.890 Fit side-chains REVERT: A 33 GLU cc_start: 0.7535 (mp0) cc_final: 0.7328 (mp0) REVERT: B 33 GLU cc_start: 0.7540 (mp0) cc_final: 0.7333 (mp0) REVERT: C 33 GLU cc_start: 0.7535 (mp0) cc_final: 0.7320 (mp0) REVERT: D 33 GLU cc_start: 0.7542 (mp0) cc_final: 0.7333 (mp0) outliers start: 20 outliers final: 8 residues processed: 176 average time/residue: 2.5097 time to fit residues: 483.0329 Evaluate side-chains 165 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12328 Z= 0.253 Angle : 0.451 4.345 16728 Z= 0.252 Chirality : 0.035 0.124 2012 Planarity : 0.004 0.025 2040 Dihedral : 3.833 22.111 1760 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.13 % Allowed : 16.41 % Favored : 81.46 % 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: 2.83 (0.21), residues: 1508 helix: 2.29 (0.14), residues: 1260 sheet: 1.38 (0.75), residues: 48 loop : -0.81 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.003 0.001 HIS D 337 PHE 0.015 0.002 PHE C 125 TYR 0.006 0.001 TYR B 182 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.904 Fit side-chains REVERT: A 33 GLU cc_start: 0.7581 (mp0) cc_final: 0.7329 (mp0) REVERT: A 423 GLN cc_start: 0.6065 (mm110) cc_final: 0.5096 (pt0) REVERT: B 33 GLU cc_start: 0.7577 (mp0) cc_final: 0.7325 (mp0) REVERT: B 423 GLN cc_start: 0.6049 (mm110) cc_final: 0.5082 (pt0) REVERT: C 33 GLU cc_start: 0.7580 (mp0) cc_final: 0.7324 (mp0) REVERT: C 423 GLN cc_start: 0.6057 (mm110) cc_final: 0.5081 (pt0) REVERT: D 33 GLU cc_start: 0.7580 (mp0) cc_final: 0.7325 (mp0) REVERT: D 423 GLN cc_start: 0.6062 (mm110) cc_final: 0.5097 (pt0) outliers start: 28 outliers final: 8 residues processed: 192 average time/residue: 2.6411 time to fit residues: 555.5648 Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12328 Z= 0.238 Angle : 0.449 4.158 16728 Z= 0.250 Chirality : 0.035 0.124 2012 Planarity : 0.004 0.024 2040 Dihedral : 3.756 20.791 1760 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 18.54 % Favored : 80.24 % 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: 2.86 (0.21), residues: 1508 helix: 2.32 (0.14), residues: 1260 sheet: 1.37 (0.75), residues: 48 loop : -0.82 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 328 HIS 0.003 0.001 HIS A 337 PHE 0.011 0.001 PHE B 298 TYR 0.005 0.001 TYR B 182 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.915 Fit side-chains REVERT: A 33 GLU cc_start: 0.7565 (mp0) cc_final: 0.7322 (mp0) REVERT: A 423 GLN cc_start: 0.6076 (mm110) cc_final: 0.5059 (pt0) REVERT: B 33 GLU cc_start: 0.7559 (mp0) cc_final: 0.7316 (mp0) REVERT: B 423 GLN cc_start: 0.6064 (mm110) cc_final: 0.5048 (pt0) REVERT: C 33 GLU cc_start: 0.7561 (mp0) cc_final: 0.7310 (mp0) REVERT: C 423 GLN cc_start: 0.6068 (mm110) cc_final: 0.5049 (pt0) REVERT: D 33 GLU cc_start: 0.7563 (mp0) cc_final: 0.7316 (mp0) REVERT: D 423 GLN cc_start: 0.6073 (mm110) cc_final: 0.5059 (pt0) outliers start: 16 outliers final: 4 residues processed: 180 average time/residue: 2.5126 time to fit residues: 495.0805 Evaluate side-chains 164 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN C 383 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12328 Z= 0.290 Angle : 0.470 4.637 16728 Z= 0.261 Chirality : 0.036 0.126 2012 Planarity : 0.004 0.035 2040 Dihedral : 3.753 13.892 1756 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.90 % Allowed : 18.62 % Favored : 79.48 % 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: 2.69 (0.21), residues: 1508 helix: 2.20 (0.14), residues: 1260 sheet: 1.39 (0.76), residues: 48 loop : -0.88 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 PHE 0.018 0.002 PHE D 125 TYR 0.006 0.001 TYR C 182 ARG 0.005 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.846 Fit side-chains REVERT: A 33 GLU cc_start: 0.7626 (mp0) cc_final: 0.7362 (mp0) REVERT: A 423 GLN cc_start: 0.6165 (mm110) cc_final: 0.5039 (pt0) REVERT: B 33 GLU cc_start: 0.7623 (mp0) cc_final: 0.7357 (mp0) REVERT: B 423 GLN cc_start: 0.6153 (mm110) cc_final: 0.5029 (pt0) REVERT: C 33 GLU cc_start: 0.7626 (mp0) cc_final: 0.7356 (mp0) REVERT: C 423 GLN cc_start: 0.6158 (mm110) cc_final: 0.5029 (pt0) REVERT: D 33 GLU cc_start: 0.7624 (mp0) cc_final: 0.7358 (mp0) REVERT: D 423 GLN cc_start: 0.6162 (mm110) cc_final: 0.5042 (pt0) outliers start: 25 outliers final: 9 residues processed: 193 average time/residue: 2.4216 time to fit residues: 512.9466 Evaluate side-chains 181 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12328 Z= 0.166 Angle : 0.426 3.758 16728 Z= 0.237 Chirality : 0.034 0.124 2012 Planarity : 0.004 0.024 2040 Dihedral : 3.419 11.392 1756 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.61 % Allowed : 19.45 % Favored : 79.94 % 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: 2.99 (0.21), residues: 1508 helix: 2.39 (0.14), residues: 1264 sheet: 1.29 (0.76), residues: 48 loop : -0.69 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.003 0.001 HIS C 337 PHE 0.009 0.001 PHE D 11 TYR 0.005 0.001 TYR B 179 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.901 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 168 average time/residue: 2.7487 time to fit residues: 502.0990 Evaluate side-chains 164 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12328 Z= 0.240 Angle : 0.456 4.224 16728 Z= 0.253 Chirality : 0.035 0.124 2012 Planarity : 0.004 0.025 2040 Dihedral : 3.546 11.668 1756 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.14 % Allowed : 19.22 % Favored : 79.64 % 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: 2.86 (0.21), residues: 1508 helix: 2.33 (0.14), residues: 1260 sheet: 1.30 (0.76), residues: 48 loop : -0.86 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.003 0.001 HIS C 337 PHE 0.019 0.002 PHE A 125 TYR 0.005 0.001 TYR C 182 ARG 0.003 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.934 Fit side-chains REVERT: A 33 GLU cc_start: 0.7545 (mp0) cc_final: 0.7321 (mp0) REVERT: A 423 GLN cc_start: 0.6212 (mm110) cc_final: 0.5057 (pt0) REVERT: B 33 GLU cc_start: 0.7542 (mp0) cc_final: 0.7319 (mp0) REVERT: C 33 GLU cc_start: 0.7545 (mp0) cc_final: 0.7317 (mp0) REVERT: D 33 GLU cc_start: 0.7544 (mp0) cc_final: 0.7319 (mp0) outliers start: 15 outliers final: 7 residues processed: 173 average time/residue: 2.5383 time to fit residues: 481.4027 Evaluate side-chains 164 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12328 Z= 0.185 Angle : 0.433 3.963 16728 Z= 0.240 Chirality : 0.034 0.124 2012 Planarity : 0.004 0.023 2040 Dihedral : 3.410 11.389 1756 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.91 % Allowed : 19.15 % Favored : 79.94 % 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: 3.01 (0.21), residues: 1508 helix: 2.41 (0.14), residues: 1264 sheet: 1.31 (0.76), residues: 48 loop : -0.74 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 154 HIS 0.003 0.001 HIS D 337 PHE 0.009 0.001 PHE A 11 TYR 0.004 0.001 TYR C 179 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.826 Fit side-chains REVERT: A 33 GLU cc_start: 0.7524 (mp0) cc_final: 0.7297 (mp0) REVERT: B 33 GLU cc_start: 0.7521 (mp0) cc_final: 0.7292 (mp0) REVERT: C 33 GLU cc_start: 0.7523 (mp0) cc_final: 0.7293 (mp0) REVERT: D 33 GLU cc_start: 0.7522 (mp0) cc_final: 0.7293 (mp0) outliers start: 12 outliers final: 8 residues processed: 171 average time/residue: 2.5605 time to fit residues: 478.8242 Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12328 Z= 0.225 Angle : 0.448 4.012 16728 Z= 0.248 Chirality : 0.034 0.124 2012 Planarity : 0.004 0.024 2040 Dihedral : 3.503 11.598 1756 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.30 % Allowed : 19.45 % Favored : 80.24 % 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: 2.91 (0.21), residues: 1508 helix: 2.34 (0.14), residues: 1264 sheet: 1.30 (0.76), residues: 48 loop : -0.76 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 PHE 0.018 0.002 PHE C 125 TYR 0.005 0.001 TYR C 182 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 1.901 Fit side-chains REVERT: A 33 GLU cc_start: 0.7542 (mp0) cc_final: 0.7312 (mp0) REVERT: A 423 GLN cc_start: 0.6103 (mm110) cc_final: 0.4994 (pt0) REVERT: B 33 GLU cc_start: 0.7537 (mp0) cc_final: 0.7306 (mp0) REVERT: C 33 GLU cc_start: 0.7543 (mp0) cc_final: 0.7306 (mp0) REVERT: D 33 GLU cc_start: 0.7541 (mp0) cc_final: 0.7307 (mp0) outliers start: 4 outliers final: 4 residues processed: 172 average time/residue: 2.5478 time to fit residues: 479.2468 Evaluate side-chains 162 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12328 Z= 0.158 Angle : 0.421 3.727 16728 Z= 0.234 Chirality : 0.033 0.124 2012 Planarity : 0.003 0.023 2040 Dihedral : 3.327 11.124 1756 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.45 % Favored : 79.94 % 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: 3.15 (0.21), residues: 1508 helix: 2.51 (0.14), residues: 1264 sheet: 1.33 (0.76), residues: 48 loop : -0.69 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.001 HIS C 337 PHE 0.009 0.001 PHE A 11 TYR 0.004 0.001 TYR B 179 ARG 0.003 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.994 Fit side-chains REVERT: A 33 GLU cc_start: 0.7531 (mp0) cc_final: 0.7305 (mp0) REVERT: B 33 GLU cc_start: 0.7527 (mp0) cc_final: 0.7299 (mp0) REVERT: C 33 GLU cc_start: 0.7533 (mp0) cc_final: 0.7299 (mp0) REVERT: D 33 GLU cc_start: 0.7529 (mp0) cc_final: 0.7298 (mp0) outliers start: 8 outliers final: 8 residues processed: 168 average time/residue: 2.6752 time to fit residues: 493.5828 Evaluate side-chains 167 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 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 = 0.3603 r_free = 0.3603 target = 0.139556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100703 restraints weight = 35774.415| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.68 r_work: 0.2931 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12328 Z= 0.142 Angle : 0.408 3.699 16728 Z= 0.227 Chirality : 0.033 0.124 2012 Planarity : 0.003 0.024 2040 Dihedral : 3.217 10.853 1756 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.76 % Favored : 79.64 % 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: 3.34 (0.22), residues: 1508 helix: 2.64 (0.14), residues: 1264 sheet: 1.35 (0.76), residues: 48 loop : -0.66 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.002 0.000 HIS D 337 PHE 0.008 0.001 PHE B 11 TYR 0.004 0.001 TYR A 179 ARG 0.003 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8654.96 seconds wall clock time: 152 minutes 5.08 seconds (9125.08 seconds total)