Starting phenix.real_space_refine on Sat Apr 6 06:14:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/04_2024/8jlp_36403_updated.pdb" } resolution = 3.23 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= 0.041 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 58 5.16 5 C 4687 2.51 5 N 1267 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "Y GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7343 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2310 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UJU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.61 Number of scatterers: 7343 At special positions: 0 Unit cell: (102.85, 132.6, 80.75, 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 58 16.00 O 1331 8.00 N 1267 7.00 C 4687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 42.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.585A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.465A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.347A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 388 removed outlier: 4.215A pdb=" N ARG A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'R' and resid 20 through 49 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 86 removed outlier: 3.839A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 85 " --> pdb=" O MET R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 125 removed outlier: 3.931A pdb=" N ILE R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET R 105 " --> pdb=" O SER R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 130 No H-bonds generated for 'chain 'R' and resid 128 through 130' Processing helix chain 'R' and resid 137 through 160 Proline residue: R 151 - end of helix removed outlier: 3.565A pdb=" N PHE R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 201 through 227 Processing helix chain 'R' and resid 247 through 277 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 303 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 318 Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 30 through 44 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.721A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.698A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.790A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 179 through 181 removed outlier: 4.634A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.921A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.766A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 936 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: 2.26 Time building geometry restraints manager: 3.12 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: 2373 1.34 - 1.46: 1768 1.46 - 1.58: 3278 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 7505 Sorted by residual: bond pdb=" C5 UJU R 401 " pdb=" N3 UJU R 401 " ideal model delta sigma weight residual 1.478 1.352 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C4 UJU R 401 " pdb=" C5 UJU R 401 " ideal model delta sigma weight residual 1.556 1.478 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C6 UJU R 401 " pdb=" N3 UJU R 401 " ideal model delta sigma weight residual 1.484 1.413 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 UJU R 401 " pdb=" C3 UJU R 401 " ideal model delta sigma weight residual 1.557 1.493 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 UJU R 401 " pdb=" C2 UJU R 401 " ideal model delta sigma weight residual 1.547 1.501 0.046 2.00e-02 2.50e+03 5.26e+00 ... (remaining 7500 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.04: 125 106.04 - 113.07: 4061 113.07 - 120.09: 2648 120.09 - 127.12: 3229 127.12 - 134.15: 94 Bond angle restraints: 10157 Sorted by residual: angle pdb=" C15 UJU R 401 " pdb=" C6 UJU R 401 " pdb=" N3 UJU R 401 " ideal model delta sigma weight residual 100.33 120.17 -19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C7 UJU R 401 " pdb=" C6 UJU R 401 " pdb=" N3 UJU R 401 " ideal model delta sigma weight residual 135.53 120.37 15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " ideal model delta sigma weight residual 110.28 116.05 -5.77 1.55e+00 4.16e-01 1.39e+01 angle pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " pdb=" CG GLU A 344 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta sigma weight residual 122.64 127.90 -5.26 1.70e+00 3.46e-01 9.56e+00 ... (remaining 10152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 4146 23.22 - 46.45: 280 46.45 - 69.67: 24 69.67 - 92.89: 11 92.89 - 116.12: 1 Dihedral angle restraints: 4462 sinusoidal: 1768 harmonic: 2694 Sorted by residual: dihedral pdb=" C11 UJU R 401 " pdb=" C12 UJU R 401 " pdb=" N4 UJU R 401 " pdb=" C13 UJU R 401 " ideal model delta sinusoidal sigma weight residual -52.93 63.19 -116.12 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C1 UJU R 401 " pdb=" C2 UJU R 401 " pdb=" C3 UJU R 401 " pdb=" C16 UJU R 401 " ideal model delta sinusoidal sigma weight residual -143.74 -53.20 -90.54 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" CB GLU A 370 " pdb=" CG GLU A 370 " pdb=" CD GLU A 370 " pdb=" OE1 GLU A 370 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 4459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 694 0.032 - 0.063: 299 0.063 - 0.095: 94 0.095 - 0.127: 44 0.127 - 0.158: 5 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA GLU A 344 " pdb=" N GLU A 344 " pdb=" C GLU A 344 " pdb=" CB GLU A 344 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1133 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 UJU R 401 " 0.060 2.00e-02 2.50e+03 6.75e-02 5.70e+01 pdb=" C5 UJU R 401 " -0.025 2.00e-02 2.50e+03 pdb=" C6 UJU R 401 " 0.081 2.00e-02 2.50e+03 pdb=" N3 UJU R 401 " -0.109 2.00e-02 2.50e+03 pdb=" O1 UJU R 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 254 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C GLY R 254 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY R 254 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE R 255 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ARG A 380 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 380 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 381 " 0.011 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 822 2.75 - 3.29: 7398 3.29 - 3.82: 11908 3.82 - 4.36: 13714 4.36 - 4.90: 23712 Nonbonded interactions: 57554 Sorted by model distance: nonbonded pdb=" NE1 TRP R 264 " pdb=" OD1 ASN R 296 " model vdw 2.209 2.520 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.212 2.440 nonbonded pdb=" O ARG A 333 " pdb=" NH1 ARG A 333 " model vdw 2.246 2.520 nonbonded pdb=" O CYS B 103 " pdb=" NH1 ARG B 150 " model vdw 2.300 2.520 nonbonded pdb=" ND2 ASN B 119 " pdb=" O THR B 143 " model vdw 2.307 2.520 ... (remaining 57549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 0.010 Normalize map: mean=0, sd=1: 0.990 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: 3.880 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.820 Find NCS groups from input model: 0.200 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 0.126 7505 Z= 0.269 Angle : 0.697 19.843 10157 Z= 0.354 Chirality : 0.043 0.158 1136 Planarity : 0.004 0.068 1284 Dihedral : 15.020 116.117 2713 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.31 (0.28), residues: 909 helix: 1.41 (0.27), residues: 383 sheet: -0.75 (0.44), residues: 139 loop : -1.68 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.002 PHE R 165 TYR 0.014 0.001 TYR A 339 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.834 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2005 time to fit residues: 31.9656 Evaluate side-chains 91 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7505 Z= 0.198 Angle : 0.569 7.696 10157 Z= 0.294 Chirality : 0.041 0.135 1136 Planarity : 0.004 0.044 1284 Dihedral : 4.569 51.451 1011 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.38 % Allowed : 9.43 % Favored : 89.18 % 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: -0.17 (0.29), residues: 909 helix: 1.52 (0.27), residues: 391 sheet: -0.80 (0.42), residues: 161 loop : -1.64 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE R 154 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7173 (mpp) cc_final: 0.6540 (mpp) REVERT: R 194 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8017 (m) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.1770 time to fit residues: 25.4678 Evaluate side-chains 102 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 20.0000 chunk 68 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7505 Z= 0.134 Angle : 0.504 8.324 10157 Z= 0.261 Chirality : 0.040 0.137 1136 Planarity : 0.003 0.044 1284 Dihedral : 4.300 50.908 1011 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.64 % Allowed : 11.82 % Favored : 86.54 % 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: 0.10 (0.29), residues: 909 helix: 1.77 (0.27), residues: 389 sheet: -0.66 (0.43), residues: 150 loop : -1.52 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE R 154 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.893 Fit side-chains REVERT: A 60 MET cc_start: 0.7261 (mpp) cc_final: 0.6844 (mpp) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.2167 time to fit residues: 32.6005 Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN A 294 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7505 Z= 0.356 Angle : 0.656 7.783 10157 Z= 0.342 Chirality : 0.045 0.151 1136 Planarity : 0.004 0.041 1284 Dihedral : 4.806 56.325 1011 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.01 % Allowed : 15.09 % Favored : 82.89 % 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: -0.23 (0.28), residues: 909 helix: 1.49 (0.26), residues: 386 sheet: -0.79 (0.45), residues: 148 loop : -1.66 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.018 0.002 PHE A 219 TYR 0.021 0.002 TYR A 37 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.817 Fit side-chains REVERT: A 289 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8009 (tt) REVERT: R 273 MET cc_start: 0.5564 (ptt) cc_final: 0.5341 (ptt) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1817 time to fit residues: 27.0566 Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 0.0070 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7505 Z= 0.158 Angle : 0.544 9.267 10157 Z= 0.279 Chirality : 0.041 0.152 1136 Planarity : 0.004 0.043 1284 Dihedral : 4.586 55.292 1011 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.64 % Allowed : 17.36 % Favored : 81.01 % 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: -0.03 (0.29), residues: 909 helix: 1.65 (0.27), residues: 390 sheet: -0.65 (0.45), residues: 148 loop : -1.60 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.003 0.001 HIS R 55 PHE 0.018 0.001 PHE A 290 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.769 Fit side-chains REVERT: A 60 MET cc_start: 0.7009 (mpp) cc_final: 0.6764 (mpt) REVERT: A 244 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7266 (mt) REVERT: B 225 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4220 (m-70) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.2071 time to fit residues: 29.5954 Evaluate side-chains 102 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN A 294 GLN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7505 Z= 0.239 Angle : 0.573 10.141 10157 Z= 0.296 Chirality : 0.042 0.152 1136 Planarity : 0.004 0.041 1284 Dihedral : 4.477 40.279 1011 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.26 % Allowed : 18.74 % Favored : 78.99 % 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: -0.07 (0.29), residues: 909 helix: 1.61 (0.26), residues: 391 sheet: -0.69 (0.45), residues: 148 loop : -1.61 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS B 225 PHE 0.020 0.001 PHE A 290 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.854 Fit side-chains REVERT: A 244 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7278 (mt) REVERT: A 289 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7904 (tt) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.1942 time to fit residues: 28.7299 Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS R 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7505 Z= 0.153 Angle : 0.544 10.479 10157 Z= 0.279 Chirality : 0.041 0.164 1136 Planarity : 0.004 0.042 1284 Dihedral : 4.344 41.136 1011 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.77 % Allowed : 18.62 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 909 helix: 1.85 (0.27), residues: 385 sheet: -0.54 (0.46), residues: 142 loop : -1.63 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.003 0.001 HIS R 55 PHE 0.015 0.001 PHE A 290 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.849 Fit side-chains REVERT: A 60 MET cc_start: 0.7135 (mpt) cc_final: 0.6771 (mpt) REVERT: A 244 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7278 (mt) REVERT: A 289 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7781 (tt) REVERT: B 225 HIS cc_start: 0.5215 (OUTLIER) cc_final: 0.4360 (m-70) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.1916 time to fit residues: 28.6115 Evaluate side-chains 107 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7505 Z= 0.266 Angle : 0.598 11.238 10157 Z= 0.307 Chirality : 0.043 0.150 1136 Planarity : 0.004 0.041 1284 Dihedral : 4.373 43.629 1011 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.77 % Allowed : 19.25 % Favored : 77.99 % 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: -0.10 (0.29), residues: 909 helix: 1.58 (0.27), residues: 391 sheet: -0.45 (0.48), residues: 136 loop : -1.72 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.017 0.001 HIS B 225 PHE 0.019 0.002 PHE A 290 TYR 0.017 0.001 TYR A 37 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.827 Fit side-chains REVERT: A 244 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7337 (mp) REVERT: A 289 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7941 (tt) REVERT: R 172 TYR cc_start: 0.7384 (t80) cc_final: 0.6986 (t80) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.1797 time to fit residues: 27.6547 Evaluate side-chains 110 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 50 HIS Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.0070 chunk 52 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 176 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7505 Z= 0.201 Angle : 0.578 12.035 10157 Z= 0.296 Chirality : 0.042 0.148 1136 Planarity : 0.004 0.042 1284 Dihedral : 4.354 49.657 1011 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.77 % Allowed : 19.37 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 909 helix: 1.65 (0.27), residues: 391 sheet: -0.41 (0.48), residues: 136 loop : -1.71 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS R 55 PHE 0.018 0.001 PHE A 290 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.610 Fit side-chains REVERT: A 244 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7248 (mt) REVERT: A 289 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7856 (tt) REVERT: R 172 TYR cc_start: 0.7371 (t80) cc_final: 0.6998 (t80) outliers start: 22 outliers final: 18 residues processed: 109 average time/residue: 0.1856 time to fit residues: 27.7598 Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 274 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7505 Z= 0.148 Angle : 0.560 12.346 10157 Z= 0.286 Chirality : 0.041 0.147 1136 Planarity : 0.004 0.043 1284 Dihedral : 4.267 52.583 1011 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.14 % Allowed : 20.00 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.29), residues: 909 helix: 1.83 (0.27), residues: 385 sheet: -0.32 (0.48), residues: 130 loop : -1.65 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS R 55 PHE 0.016 0.001 PHE R 165 TYR 0.011 0.001 TYR B 264 ARG 0.003 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.815 Fit side-chains REVERT: A 244 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 289 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (tt) REVERT: B 176 GLN cc_start: 0.7193 (tt0) cc_final: 0.6675 (mt0) REVERT: R 172 TYR cc_start: 0.7311 (t80) cc_final: 0.6971 (t80) REVERT: R 194 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8279 (m) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.1853 time to fit residues: 26.6478 Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 274 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.0000 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.247964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.202016 restraints weight = 7831.755| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.76 r_work: 0.4134 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7505 Z= 0.158 Angle : 0.557 12.609 10157 Z= 0.284 Chirality : 0.041 0.147 1136 Planarity : 0.003 0.043 1284 Dihedral : 4.222 53.256 1011 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.89 % Allowed : 19.75 % Favored : 77.36 % 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: 0.11 (0.29), residues: 909 helix: 1.85 (0.27), residues: 385 sheet: -0.29 (0.49), residues: 125 loop : -1.66 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS R 55 PHE 0.015 0.001 PHE R 165 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.08 seconds wall clock time: 33 minutes 45.20 seconds (2025.20 seconds total)