Starting phenix.real_space_refine on Mon Sep 23 20:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/09_2024/8ez7_28729.cif" } resolution = 2.6 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= -0.001 sd= 0.202 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 28 5.16 5 C 3065 2.51 5 N 845 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4927 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 372} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.35, per 1000 atoms: 0.88 Number of scatterers: 4927 At special positions: 0 Unit cell: (95.4, 83.74, 89.04, 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 28 16.00 O 989 8.00 N 845 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 4.8% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.744A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.585A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.547A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.784A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.412A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.090A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.648A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 124 removed outlier: 5.343A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL A 122 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N CYS A 124 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.276A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.733A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.637A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.321A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.561A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 429 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: 1.74 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1609 1.34 - 1.46: 1256 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5038 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 2.03e+00 ... (remaining 5033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 6605 1.43 - 2.87: 191 2.87 - 4.30: 25 4.30 - 5.74: 7 5.74 - 7.17: 8 Bond angle restraints: 6836 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 115.33 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 113.47 -2.77 1.22e+00 6.72e-01 5.14e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.51 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sigma weight residual 113.65 110.51 3.14 1.47e+00 4.63e-01 4.56e+00 ... (remaining 6831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 2853 23.46 - 46.93: 196 46.93 - 70.39: 28 70.39 - 93.85: 15 93.85 - 117.31: 11 Dihedral angle restraints: 3103 sinusoidal: 1336 harmonic: 1767 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 134.03 -41.03 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 54.35 -117.31 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 3100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 754 0.126 - 0.252: 5 0.252 - 0.378: 1 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 761 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 758 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.121 2.00e-02 2.50e+03 1.70e-01 3.63e+02 pdb=" CG ASN A 329 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.299 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 126 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO L 95 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.017 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 325 2.73 - 3.27: 4643 3.27 - 3.81: 8984 3.81 - 4.36: 11401 4.36 - 4.90: 19097 Nonbonded interactions: 44450 Sorted by model distance: nonbonded pdb=" OG SER A 179 " pdb=" OE2 GLU A 227 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 27A" pdb=" O ASP A 309 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" OG SER A 311 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 399 " pdb=" OG SER A 457 " model vdw 2.259 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.290 3.040 ... (remaining 44445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.34 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: 9.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 0.085 5038 Z= 0.270 Angle : 0.611 7.172 6836 Z= 0.311 Chirality : 0.051 0.630 761 Planarity : 0.004 0.044 876 Dihedral : 18.250 117.313 1950 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.10 (0.34), residues: 618 helix: 0.60 (2.68), residues: 6 sheet: -0.05 (0.32), residues: 249 loop : 0.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.556 Fit side-chains REVERT: A 277 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8125 (mt-10) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 1.2739 time to fit residues: 108.1455 Evaluate side-chains 78 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5038 Z= 0.174 Angle : 0.578 9.278 6836 Z= 0.303 Chirality : 0.049 0.417 761 Planarity : 0.004 0.043 876 Dihedral : 13.193 103.212 873 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 15.63 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.19 (0.33), residues: 618 helix: 0.28 (2.42), residues: 6 sheet: -0.02 (0.31), residues: 247 loop : -0.11 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 PHE 0.012 0.001 PHE A 354 TYR 0.011 0.001 TYR A 121 ARG 0.002 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.653 Fit side-chains REVERT: H 38 ARG cc_start: 0.9013 (ptt180) cc_final: 0.8806 (ptt180) REVERT: L 100 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: A 277 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8019 (mt-10) REVERT: A 430 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7694 (mmt-90) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 1.1564 time to fit residues: 99.2584 Evaluate side-chains 75 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5038 Z= 0.245 Angle : 0.595 9.555 6836 Z= 0.313 Chirality : 0.049 0.408 761 Planarity : 0.004 0.044 876 Dihedral : 10.962 99.661 867 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.58 % Allowed : 15.63 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.22 (0.33), residues: 618 helix: 0.23 (2.37), residues: 6 sheet: -0.03 (0.31), residues: 232 loop : -0.14 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.548 Fit side-chains REVERT: A 277 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 368 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: A 430 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7786 (mmt-90) outliers start: 19 outliers final: 10 residues processed: 81 average time/residue: 1.2217 time to fit residues: 103.7905 Evaluate side-chains 79 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5038 Z= 0.289 Angle : 0.610 9.713 6836 Z= 0.323 Chirality : 0.050 0.416 761 Planarity : 0.004 0.045 876 Dihedral : 10.206 97.140 867 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 15.82 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.29 (0.33), residues: 618 helix: 0.19 (2.39), residues: 6 sheet: -0.06 (0.31), residues: 230 loop : -0.20 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.014 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.608 Fit side-chains REVERT: L 100 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: A 277 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 368 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 430 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7837 (mmt-90) outliers start: 18 outliers final: 10 residues processed: 78 average time/residue: 1.0971 time to fit residues: 89.5467 Evaluate side-chains 81 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5038 Z= 0.339 Angle : 0.632 9.907 6836 Z= 0.336 Chirality : 0.050 0.417 761 Planarity : 0.004 0.046 876 Dihedral : 10.049 95.402 867 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.14 % Allowed : 15.63 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.44 (0.32), residues: 618 helix: 0.19 (2.41), residues: 6 sheet: -0.22 (0.31), residues: 224 loop : -0.27 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.014 0.002 TYR A 121 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.536 Fit side-chains REVERT: L 100 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: A 277 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 368 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: A 430 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (mmt-90) outliers start: 22 outliers final: 12 residues processed: 83 average time/residue: 1.0374 time to fit residues: 90.3816 Evaluate side-chains 83 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5038 Z= 0.376 Angle : 0.652 10.025 6836 Z= 0.348 Chirality : 0.051 0.422 761 Planarity : 0.005 0.046 876 Dihedral : 10.063 94.386 867 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.77 % Allowed : 16.76 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.52 (0.32), residues: 618 helix: 0.20 (2.46), residues: 6 sheet: -0.28 (0.31), residues: 224 loop : -0.33 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.014 0.002 TYR A 121 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.615 Fit side-chains REVERT: L 100 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 162 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 277 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 368 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 430 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7988 (mmt-90) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 1.2167 time to fit residues: 111.8600 Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5038 Z= 0.223 Angle : 0.589 10.295 6836 Z= 0.311 Chirality : 0.048 0.404 761 Planarity : 0.004 0.045 876 Dihedral : 9.357 91.452 867 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 17.33 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.38 (0.33), residues: 618 helix: 0.24 (2.45), residues: 6 sheet: -0.10 (0.32), residues: 232 loop : -0.28 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.558 Fit side-chains REVERT: L 100 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: A 277 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8100 (mt-10) REVERT: A 368 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: A 430 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7786 (mmt-90) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 1.1176 time to fit residues: 96.9814 Evaluate side-chains 82 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5038 Z= 0.171 Angle : 0.560 10.720 6836 Z= 0.295 Chirality : 0.047 0.390 761 Planarity : 0.004 0.044 876 Dihedral : 8.716 86.684 867 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.82 % Allowed : 17.89 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.30 (0.33), residues: 618 helix: 0.33 (2.47), residues: 6 sheet: -0.03 (0.32), residues: 237 loop : -0.25 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 184 PHE 0.013 0.001 PHE A 354 TYR 0.010 0.001 TYR A 121 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.569 Fit side-chains REVERT: L 100 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: A 277 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7903 (mt-10) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 1.2277 time to fit residues: 102.6230 Evaluate side-chains 77 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 60 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: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5038 Z= 0.221 Angle : 0.581 11.118 6836 Z= 0.305 Chirality : 0.047 0.377 761 Planarity : 0.004 0.044 876 Dihedral : 8.499 81.312 867 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.26 % Allowed : 19.40 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.26 (0.33), residues: 618 helix: 0.25 (2.38), residues: 6 sheet: 0.01 (0.32), residues: 232 loop : -0.22 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.620 Fit side-chains REVERT: L 100 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: A 277 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8034 (mt-10) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 1.1880 time to fit residues: 97.0854 Evaluate side-chains 81 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5038 Z= 0.227 Angle : 0.590 11.483 6836 Z= 0.309 Chirality : 0.047 0.338 761 Planarity : 0.004 0.045 876 Dihedral : 8.172 71.728 867 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.88 % Allowed : 19.77 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.29 (0.33), residues: 618 helix: 0.27 (2.40), residues: 6 sheet: -0.02 (0.32), residues: 232 loop : -0.25 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.002 TYR A 121 ARG 0.006 0.000 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.580 Fit side-chains REVERT: L 100 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: A 277 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 308 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8134 (mttt) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 1.2617 time to fit residues: 98.7830 Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 ASN ** L 6 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 = 0.3477 r_free = 0.3477 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107600 restraints weight = 4819.180| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.40 r_work: 0.2986 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5038 Z= 0.303 Angle : 0.634 11.421 6836 Z= 0.333 Chirality : 0.048 0.262 761 Planarity : 0.004 0.045 876 Dihedral : 8.088 54.915 867 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.26 % Allowed : 19.59 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.42 (0.33), residues: 618 helix: 0.21 (2.40), residues: 6 sheet: -0.20 (0.32), residues: 226 loop : -0.26 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.014 0.002 TYR A 121 ARG 0.006 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.58 seconds wall clock time: 45 minutes 55.04 seconds (2755.04 seconds total)